7K89

Crystal structure of bovine RPE65 in complex with 4-fluoro-emixustat and palmitate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4RSE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP281.15Same as for entry 4RSE
Crystal Properties
Matthews coefficientSolvent content
3.1560.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 175.695α = 90
b = 175.695β = 90
c = 86.214γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.979460SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.155099.90.1660.9969.86.882432
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.281.770.408

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT4RSE2.1547.8478245418799.90.190390.188930.21718RANDOM41.694
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]
0.560.280.56-1.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.251
r_dihedral_angle_4_deg14.005
r_dihedral_angle_3_deg10.535
r_dihedral_angle_1_deg7.157
r_long_range_B_other4.681
r_long_range_B_refined4.68
r_mcangle_it2.346
r_mcangle_other2.346
r_scangle_other2.172
r_mcbond_it1.328
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.251
r_dihedral_angle_4_deg14.005
r_dihedral_angle_3_deg10.535
r_dihedral_angle_1_deg7.157
r_long_range_B_other4.681
r_long_range_B_refined4.68
r_mcangle_it2.346
r_mcangle_other2.346
r_scangle_other2.172
r_mcbond_it1.328
r_mcbond_other1.327
r_scbond_it1.232
r_scbond_other1.232
r_angle_refined_deg1.174
r_angle_other_deg1.057
r_chiral_restr0.041
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8144
Nucleic Acid Atoms
Solvent Atoms800
Heterogen Atoms106

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing