5NTT

Crystal structure of human Mps1 (TTK) C604Y mutant in complex with NMS-P715


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5MRB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.429110.5% (w/v) PEG 350 MME, 10 mM MgCl2, and 100 mM Tris/HCl
Crystal Properties
Matthews coefficientSolvent content
3.4464.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.672α = 90
b = 112.01β = 90
c = 116.126γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-03-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.07227ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.7541.651000.150.1650.0670.9969.65.912326
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.752.91001.4371.580.6510.5715.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5MRB2.7541.651174857799.920.20060.19920.2298RANDOM73.976
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]
0.96-2.271.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.273
r_dihedral_angle_4_deg23.539
r_dihedral_angle_3_deg13.997
r_dihedral_angle_1_deg6.737
r_angle_refined_deg1.235
r_angle_other_deg0.868
r_chiral_restr0.069
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.273
r_dihedral_angle_4_deg23.539
r_dihedral_angle_3_deg13.997
r_dihedral_angle_1_deg6.737
r_angle_refined_deg1.235
r_angle_other_deg0.868
r_chiral_restr0.069
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2270
Nucleic Acid Atoms
Solvent Atoms32
Heterogen Atoms57

Software

Software
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing