☰ Navigation Tabs
Crystal structure of RPE65 in complex with emixustat and palmitate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FSN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 281 30% PEG200
200 mM ammonium phosphate
100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties Matthews coefficient Solvent content 3.17 61.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 175.891 α = 90 b = 175.891 β = 90 c = 86.533 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 CCD ADSC QUANTUM 315r 2014-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0750 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 50 99.54 139166 139163 -3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 3FSN 1.8 47.93 139163 132075 7088 99.54 0.16623 0.16463 0.1741 0.19569 0.2022 RANDOM 33.394
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] 0.3 0.15 0.3 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.418 r_dihedral_angle_4_deg 14.935 r_dihedral_angle_3_deg 11.926 r_sphericity_bonded 9.203 r_long_range_B_refined 7.703 r_long_range_B_other 7.414 r_dihedral_angle_1_deg 6.684 r_scangle_other 4.991 r_mcangle_it 3.941 r_mcangle_other 3.941
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.418 r_dihedral_angle_4_deg 14.935 r_dihedral_angle_3_deg 11.926 r_sphericity_bonded 9.203 r_long_range_B_refined 7.703 r_long_range_B_other 7.414 r_dihedral_angle_1_deg 6.684 r_scangle_other 4.991 r_mcangle_it 3.941 r_mcangle_other 3.941 r_scbond_it 3.209 r_scbond_other 3.208 r_mcbond_it 2.681 r_mcbond_other 2.677 r_angle_refined_deg 1.549 r_angle_other_deg 0.918 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8134 Nucleic Acid Atoms Solvent Atoms 1004 Heterogen Atoms 76
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction REFMAC phasing