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Crystal structure of RPE65 in complex with 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 40% PEG 300, 200 mM NaCl, 100 mM CHES, pH 9.5
Crystal Properties Matthews coefficient Solvent content 3.16 61.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 175.73 α = 90 b = 175.73 β = 90 c = 86.37 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 2015-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97919 APS 24-ID-E
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 2.2 50 100 0.209 11.3 12.1 77111
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 2.2 47.88 73171 3938 99.98 0.17236 0.17034 0.1805 0.20942 0.212 RANDOM 43.849
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] 0.08 0.04 0.08 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.24 r_dihedral_angle_4_deg 16.38 r_dihedral_angle_3_deg 13.006 r_sphericity_bonded 12.067 r_dihedral_angle_1_deg 7.25 r_long_range_B_refined 6.566 r_long_range_B_other 6.556 r_scangle_other 5.091 r_mcangle_it 4.09 r_mcangle_other 4.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.24 r_dihedral_angle_4_deg 16.38 r_dihedral_angle_3_deg 13.006 r_sphericity_bonded 12.067 r_dihedral_angle_1_deg 7.25 r_long_range_B_refined 6.566 r_long_range_B_other 6.556 r_scangle_other 5.091 r_mcangle_it 4.09 r_mcangle_other 4.09 r_scbond_it 3.357 r_scbond_other 3.356 r_mcbond_it 2.809 r_mcbond_other 2.809 r_angle_refined_deg 1.551 r_angle_other_deg 0.957 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8261 Nucleic Acid Atoms Solvent Atoms 447 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing