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Crystal structure of bovine RPE65 in complex with gem-difluoro emixustat and palmitate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RSC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 281 30% PEG200,
100 mM Tris pH 8.5,
200 mM ammonium phosphate
Crystal Properties Matthews coefficient Solvent content 3.15 60.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 175.425 α = 90 b = 175.425 β = 90 c = 86.668 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2020-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979180 APS 24-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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.9 50 99.7 0.113 0.999 13.1 10.4 118471 45
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) Redundancy Number Unique Reflections (All) 1 1.9 2.02 2.482 0.43 0.96
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 4RSC 1.9 47.87 112436 6033 99.74 0.1782 0.177 0.1836 0.2008 0.2052 RANDOM 44.77
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] 0.64 0.32 0.64 -2.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.515 r_dihedral_angle_4_deg 12.431 r_dihedral_angle_3_deg 11.354 r_dihedral_angle_1_deg 7.419 r_angle_refined_deg 1.214 r_angle_other_deg 1.116 r_chiral_restr 0.048 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.515 r_dihedral_angle_4_deg 12.431 r_dihedral_angle_3_deg 11.354 r_dihedral_angle_1_deg 7.419 r_angle_refined_deg 1.214 r_angle_other_deg 1.116 r_chiral_restr 0.048 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8119 Nucleic Acid Atoms Solvent Atoms 844 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling REFMAC phasing