6ZK0

1.47A human IMPase with ebselen


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6GJ0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52930.2M MnS04, 0.1M MES, 28% PEG4000 and pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.5251.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.02α = 90
b = 84.02β = 90
c = 150.22γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2019-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91188DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.4724.441000.0530.022120.411104886
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)
11.471.52.0192.1230.6520.4981.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE R-VALUE6gj01.4724.438104821508199.9660.1810.17910.208330.088
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]
-0.032-0.016-0.0320.103
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.5
r_dihedral_angle_4_deg14.469
r_dihedral_angle_3_deg13.783
r_dihedral_angle_1_deg8.411
r_lrange_it6.854
r_scangle_it5.276
r_scbond_it3.84
r_mcangle_it3.536
r_mcbond_it2.567
r_angle_refined_deg1.901
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.5
r_dihedral_angle_4_deg14.469
r_dihedral_angle_3_deg13.783
r_dihedral_angle_1_deg8.411
r_lrange_it6.854
r_scangle_it5.276
r_scbond_it3.84
r_mcangle_it3.536
r_mcbond_it2.567
r_angle_refined_deg1.901
r_metal_ion_refined0.359
r_nbtor_refined0.323
r_xyhbond_nbd_refined0.276
r_nbd_refined0.241
r_symmetry_nbd_refined0.239
r_symmetry_xyhbond_nbd_refined0.235
r_chiral_restr0.14
r_symmetry_metal_ion_refined0.109
r_bond_refined_d0.011
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4106
Nucleic Acid Atoms
Solvent Atoms426
Heterogen Atoms122

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing