7L0E

Crystal structure of bovine RPE65 in complex with gem-difluoro emixustat and palmitate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP28130% PEG200, 100 mM Tris pH 8.5, 200 mM ammonium phosphate
Crystal Properties
Matthews coefficientSolvent content
3.1560.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 175.425α = 90
b = 175.425β = 90
c = 86.668γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-10-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.979180APS24-ID-E

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
11.95099.70.1130.99913.110.411847145
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)
11.92.022.4820.430.96

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 SYNTHESISTHROUGHOUT4RSC1.947.87112436603399.740.17820.1770.2008RANDOM44.77
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]
0.640.320.64-2.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.515
r_dihedral_angle_4_deg12.431
r_dihedral_angle_3_deg11.354
r_dihedral_angle_1_deg7.419
r_angle_refined_deg1.214
r_angle_other_deg1.116
r_chiral_restr0.048
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.515
r_dihedral_angle_4_deg12.431
r_dihedral_angle_3_deg11.354
r_dihedral_angle_1_deg7.419
r_angle_refined_deg1.214
r_angle_other_deg1.116
r_chiral_restr0.048
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8119
Nucleic Acid Atoms
Solvent Atoms844
Heterogen Atoms85

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
REFMACphasing