9FAY

Gcase in complex with small molecule inhibitor 1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1M KSCN 25% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.1542.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.878α = 90
b = 74.481β = 102.63
c = 68.359γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-10-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X1A1.00003NSLSX1A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
11.38966.7186.70.05213.53.464808
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.3891.5580.82

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1.466.7162705317865.260.14980.148120.1831RANDOM23.787
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]
0.160.07-0.530.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.685
r_dihedral_angle_4_deg14.064
r_dihedral_angle_3_deg12.8
r_dihedral_angle_1_deg11.27
r_long_range_B_refined5.193
r_long_range_B_other5.052
r_scbond_it2.737
r_scbond_other2.737
r_angle_refined_deg1.515
r_mcbond_it1.269
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.685
r_dihedral_angle_4_deg14.064
r_dihedral_angle_3_deg12.8
r_dihedral_angle_1_deg11.27
r_long_range_B_refined5.193
r_long_range_B_other5.052
r_scbond_it2.737
r_scbond_other2.737
r_angle_refined_deg1.515
r_mcbond_it1.269
r_mcbond_other1.269
r_angle_other_deg0.529
r_chiral_restr0.077
r_bond_refined_d0.01
r_bond_other_d0.001
r_gen_planes_refined0.001
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_it
r_mcangle_other
r_scangle_it
r_scangle_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3930
Nucleic Acid Atoms
Solvent Atoms627
Heterogen Atoms121

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing