4YPD | pdb_00004ypd

Crystal Structure of DAPK1 catalytic domain in complex with the hinge binding fragment 4-methylpyridazine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JKS	PDB entry 1JKS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	0.1 M HEPES, 1.7 M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.853	α = 90
b = 62.511	β = 90
c = 88.193	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	CCD	MARMOSAIC 300 mm CCD		2011-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.978	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.35	30	99.5	23.33	7.2		57841

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.35

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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 entry 1JKS	1.4	29.46	48902	2610	99.48	0.1562	0.1551	0.16	0.1772	0.19	RANDOM	24.216

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]
0.42			0.32		-0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.542
r_dihedral_angle_4_deg	13.146
r_dihedral_angle_3_deg	10.558
r_dihedral_angle_1_deg	4.232
r_mcangle_it	2.259
r_mcbond_it	1.474
r_mcbond_other	1.472
r_angle_refined_deg	1.443
r_angle_other_deg	0.773
r_chiral_restr	0.095

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.542
r_dihedral_angle_4_deg	13.146
r_dihedral_angle_3_deg	10.558
r_dihedral_angle_1_deg	4.232
r_mcangle_it	2.259
r_mcbond_it	1.474
r_mcbond_other	1.472
r_angle_refined_deg	1.443
r_angle_other_deg	0.773
r_chiral_restr	0.095
r_gen_planes_refined	0.021
r_gen_planes_other	0.017
r_bond_refined_d	0.01
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2283
Nucleic Acid Atoms
Solvent Atoms	325
Heterogen Atoms	21

Software

Software
Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

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.