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Crystal structure of RPE65 in complex with MB-001 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 9.5 281 40% PEG 300
200 mM NaCl
100 mM CHES-NAOH, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties Matthews coefficient Solvent content 3.16 61.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 175.639 α = 90 b = 175.639 β = 90 c = 86.611 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 2014-08-22 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 2.39 50 99.15 59881 59880 -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 2.39 47.9 59880 56801 3079 99.15 0.19784 0.19576 0.2013 0.2357 0.2356 RANDOM 47.059
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] 0.54 0.27 0.54 -1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.122 r_sphericity_bonded 18.333 r_dihedral_angle_4_deg 17.243 r_dihedral_angle_3_deg 13.885 r_dihedral_angle_1_deg 6.939 r_long_range_B_refined 6.6 r_long_range_B_other 6.558 r_scangle_other 4.197 r_mcangle_it 3.975 r_mcangle_other 3.975
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.122 r_sphericity_bonded 18.333 r_dihedral_angle_4_deg 17.243 r_dihedral_angle_3_deg 13.885 r_dihedral_angle_1_deg 6.939 r_long_range_B_refined 6.6 r_long_range_B_other 6.558 r_scangle_other 4.197 r_mcangle_it 3.975 r_mcangle_other 3.975 r_scbond_it 2.555 r_scbond_other 2.555 r_mcbond_it 2.43 r_mcbond_other 2.429 r_angle_refined_deg 1.398 r_angle_other_deg 0.979 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8250 Nucleic Acid Atoms Solvent Atoms 401 Heterogen Atoms 82
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction REFMAC phasing