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Crystal structure of bovine RPE65 in complex with EYE-002
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% PEG 200, 200 mM ammonium phosphate
Crystal Properties Matthews coefficient Solvent content 3.16 61.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 175.81 α = 90 b = 175.81 β = 90 c = 86.46 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 2024-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.979460 SSRL BL12-2
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 2.1 50 98.8 0.153 0.997 8.5 10 87750
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 2.1 2.22 2.025 0.298 0.8
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 2.1 47.906 87750 4497 98.77 0.182 0.1801 0.187 0.2089 0.2141 46.496
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] 0.828 0.414 0.828 -2.687
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.373 r_dihedral_angle_3_deg 9.511 r_lrange_it 6.841 r_lrange_other 6.84 r_dihedral_angle_1_deg 6.806 r_dihedral_angle_2_deg 3.992 r_scangle_it 3.581 r_scangle_other 3.581 r_mcangle_other 3.245 r_mcangle_it 3.244
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.373 r_dihedral_angle_3_deg 9.511 r_lrange_it 6.841 r_lrange_other 6.84 r_dihedral_angle_1_deg 6.806 r_dihedral_angle_2_deg 3.992 r_scangle_it 3.581 r_scangle_other 3.581 r_mcangle_other 3.245 r_mcangle_it 3.244 r_scbond_it 2.086 r_scbond_other 2.086 r_mcbond_it 1.9 r_mcbond_other 1.898 r_angle_refined_deg 0.914 r_angle_other_deg 0.334 r_symmetry_nbd_other 0.175 r_nbtor_refined 0.175 r_nbd_refined 0.171 r_nbd_other 0.162 r_symmetry_xyhbond_nbd_refined 0.159 r_symmetry_nbd_refined 0.148 r_xyhbond_nbd_refined 0.124 r_metal_ion_refined 0.096 r_symmetry_nbtor_other 0.078 r_ncsr_local_group_1 0.056 r_chiral_restr 0.047 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8153 Nucleic Acid Atoms Solvent Atoms 987 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing