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Crystal structure of bovine RPE65 in complex with 4-fluoro-MB-004 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 281.15 Same as for entry 4RSC
Crystal Properties Matthews coefficient Solvent content 3.37 63.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 175.511 α = 90 b = 175.511 β = 90 c = 86.657 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 2020-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979358 NSLS-II 17-ID-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 1.95 50 99.7 0.163 0.998 11 11 110605
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 1.95 2.07 2.346 0.463
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 1.95 47.88 104965 5639 99.65 0.19472 0.19383 0.1988 0.21105 0.2172 RANDOM 37.105
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] 0.61 0.3 0.61 -1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.074 r_dihedral_angle_1_deg 15.311 r_dihedral_angle_4_deg 12.804 r_dihedral_angle_3_deg 10.645 r_long_range_B_refined 4.514 r_long_range_B_other 4.514 r_mcangle_it 2.006 r_mcangle_other 2.005 r_scangle_other 1.789 r_angle_refined_deg 1.168
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.074 r_dihedral_angle_1_deg 15.311 r_dihedral_angle_4_deg 12.804 r_dihedral_angle_3_deg 10.645 r_long_range_B_refined 4.514 r_long_range_B_other 4.514 r_mcangle_it 2.006 r_mcangle_other 2.005 r_scangle_other 1.789 r_angle_refined_deg 1.168 r_mcbond_it 1.134 r_mcbond_other 1.132 r_angle_other_deg 1.066 r_scbond_it 1.038 r_scbond_other 1.038 r_chiral_restr 0.041 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 8068 Nucleic Acid Atoms Solvent Atoms 851 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing