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Crystal structure of bovine RPE65 in complex with an emixustat azolog
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 8.5 281 100 mM Tris-HCl, pH 8.5,
30% v/v PEG 200,
200 mM (NH4)2HPO4
Crystal Properties Matthews coefficient Solvent content 3.16 61.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 175.72 α = 90 b = 175.72 β = 90 c = 86.59 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 EIGER2 X 16M 2024-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 0.979460 SSRL BL12-1
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 1.75 50 100 0.0108 0.999 14.75 13.1 153073
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 1.75 1.85 3.478 0.218 0.56
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.75 47.911 153071 7758 99.975 0.15 0.1479 0.158 0.1812 0.1858 37.232
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] 0.349 0.174 0.349 -1.131
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.08 r_lrange_other 17.066 r_dihedral_angle_6_deg 14.199 r_dihedral_angle_3_deg 10.456 r_scangle_it 9.198 r_scangle_other 9.197 r_mcangle_it 8.096 r_mcangle_other 8.096 r_dihedral_angle_1_deg 7.721 r_scbond_it 5.991
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.08 r_lrange_other 17.066 r_dihedral_angle_6_deg 14.199 r_dihedral_angle_3_deg 10.456 r_scangle_it 9.198 r_scangle_other 9.197 r_mcangle_it 8.096 r_mcangle_other 8.096 r_dihedral_angle_1_deg 7.721 r_scbond_it 5.991 r_scbond_other 5.991 r_dihedral_angle_2_deg 5.744 r_mcbond_it 5.264 r_mcbond_other 5.262 r_rigid_bond_restr 1.956 r_angle_refined_deg 0.934 r_angle_other_deg 0.345 r_nbd_other 0.213 r_nbd_refined 0.194 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.132 r_symmetry_nbd_refined 0.128 r_symmetry_xyhbond_nbd_refined 0.115 r_symmetry_nbtor_other 0.081 r_ncsr_local_group_1 0.054 r_chiral_restr 0.05 r_symmetry_xyhbond_nbd_other 0.037 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8034 Nucleic Acid Atoms Solvent Atoms 980 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing