2ZMD | pdb_00002zmd

Crystal structure of human Mps1 catalytic domain T686A mutant in complex with SP600125 inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ZMC	PDB ENTRY 2ZMC

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
2.34	47.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.6	α = 90
b = 105.17	β = 90
c = 111.97	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	94	IMAGE PLATE	RIGAKU RAXIS IV++		2007-09-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	2.88	59.76	99.8	0.107	0.072	11.7	3.1		9729		1	84.702

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	2.88	3.04	100		0.798	0.535	1.5	3.1	1397

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 2ZMC	2.88	40.49	9729	9261	468	99.61	0.22314	0.22122	0.23	0.2605	0.27	RANDOM	50.441

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]
-3.78			0.73		3.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.778
r_dihedral_angle_4_deg	23.639
r_dihedral_angle_3_deg	14.003
r_dihedral_angle_1_deg	5.537
r_angle_refined_deg	1.023
r_angle_other_deg	0.786
r_scangle_it	0.537
r_mcangle_it	0.373
r_scbond_it	0.354
r_mcbond_it	0.332
r_symmetry_vdw_refined	0.2
r_nbd_refined	0.194
r_symmetry_vdw_other	0.183
r_nbtor_refined	0.174
r_nbd_other	0.165
r_symmetry_hbond_refined	0.131
r_xyhbond_nbd_refined	0.122
r_nbtor_other	0.082
r_chiral_restr	0.062
r_mcbond_other	0.03
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2111
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms	33

Software

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