2ZMC | pdb_00002zmc

Crystal structure of human mitotic checkpoint kinase Mps1 catalytic domain apo form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PHK	PDB ENTRY 1PHK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	PEG300, HEPES, pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.43	α = 90
b = 103.94	β = 90
c = 110.55	γ = 90

Symmetry
Space Group	I 2 2 2

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	ADSC QUANTUM 315	mirrors	2007-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9200	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	3.14	59.44	96.4	0.123	0.056	13.1	5.2		7029		1	84.992

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.14	3.31	96.4		0.636	0.283	2.8	5.3	1030

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 1PHK	3.14	59.4	7029	6697	332	95.21	0.22603	0.22279	0.23	0.28902	0.29	RANDOM	58.85

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]
-5.29			-2.62		7.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.752
r_dihedral_angle_4_deg	22.698
r_dihedral_angle_3_deg	15.596
r_dihedral_angle_1_deg	6.375
r_angle_refined_deg	1.076
r_angle_other_deg	0.775
r_scangle_it	0.66
r_scbond_it	0.45
r_mcangle_it	0.418
r_mcbond_it	0.375
r_symmetry_hbond_refined	0.293
r_symmetry_vdw_refined	0.229
r_nbd_refined	0.212
r_symmetry_vdw_other	0.192
r_nbtor_refined	0.18
r_nbd_other	0.174
r_xyhbond_nbd_refined	0.102
r_nbtor_other	0.084
r_chiral_restr	0.06
r_mcbond_other	0.031
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2121
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing