3P1A | pdb_00003p1a

Structure of human Membrane-associated Tyrosine- and Threonine-specific cdc2-inhibitory kinase MYT1 (PKMYT1)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C30	PDB ENTRIES 2C30 and 3CR0
experimental model	PDB	3CR0	PDB ENTRIES 2C30 and 3CR0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293.15	20% PEG 3350, 0.2M KSCN, 0.1M Bis-Tris Propane, pH 6.5, 10% Ethylene glycol , VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.4	α = 90
b = 56.3	β = 90
c = 114.66	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 2M	Kirkpatrick Baez bimorph mirror pair	2010-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9245	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.7	35.32	98.6	0.087	13.2	6.2	32606	32553			15.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.7	1.79	95.3		0.445	3.2	4	4497

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 2C30 and 3CR0	1.7	30.08	2	32553	30914	1639	98.32	0.1522	0.1522	0.14995	0.16	0.19495	0.2	RANDOM	14.802

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.32			0.79		-0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.81
r_dihedral_angle_4_deg	18.656
r_dihedral_angle_3_deg	11.539
r_scangle_it	8.994
r_scbond_it	6.631
r_dihedral_angle_1_deg	5.154
r_mcangle_it	4.161
r_mcbond_it	2.762
r_angle_refined_deg	1.56
r_angle_other_deg	0.985

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.81
r_dihedral_angle_4_deg	18.656
r_dihedral_angle_3_deg	11.539
r_scangle_it	8.994
r_scbond_it	6.631
r_dihedral_angle_1_deg	5.154
r_mcangle_it	4.161
r_mcbond_it	2.762
r_angle_refined_deg	1.56
r_angle_other_deg	0.985
r_mcbond_other	0.842
r_chiral_restr	0.098
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2170
Nucleic Acid Atoms
Solvent Atoms	350
Heterogen Atoms	48

Software

Software
Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.