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Crystal structure of RPE65 in complex with S-emixustat and palmitate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.5 281 40% PEG 300, 200 mM NaCl, 100 mM CHES, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties Matthews coefficient Solvent content 3.15 60.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 175.603 α = 90 b = 175.603 β = 90 c = 86.323 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 PILATUS 6M-F 2014-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97910 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.5 50 96.2 0.117 10.11 2.6 50434 50434 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.65 94.7 0.915 1.1 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 rigid body refinement THROUGHOUT 2.5 47.84 50434 50434 2585 96.19 0.17906 0.17687 0.1841 0.21906 0.2197 RANDOM 42.877
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] 0.69 0.35 0.69 -2.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.472 r_dihedral_angle_4_deg 16.253 r_dihedral_angle_3_deg 14.507 r_long_range_B_refined 7.209 r_dihedral_angle_1_deg 7.142 r_long_range_B_other 7.122 r_scangle_other 4.679 r_mcangle_it 4.208 r_mcangle_other 4.207 r_scbond_it 2.861
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.472 r_dihedral_angle_4_deg 16.253 r_dihedral_angle_3_deg 14.507 r_long_range_B_refined 7.209 r_dihedral_angle_1_deg 7.142 r_long_range_B_other 7.122 r_scangle_other 4.679 r_mcangle_it 4.208 r_mcangle_other 4.207 r_scbond_it 2.861 r_scbond_other 2.86 r_mcbond_it 2.577 r_mcbond_other 2.576 r_angle_refined_deg 1.491 r_angle_other_deg 1.036 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.003 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 8250 Nucleic Acid Atoms Solvent Atoms 444 Heterogen Atoms 76
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction REFMAC phasing