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Crystal structure of D477G ACO/RPE65 chimera, trigonal crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6C7K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 281 0.1 M Bis-Tris propane, pH 6 and 21% w/v sodium polyacrylate 2100
Crystal Properties Matthews coefficient Solvent content 3.39 63.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.52 α = 90 b = 126.52 β = 90 c = 159.67 γ = 120
Symmetry Space Group P 3 1 2
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 EIGER X 16M 2017-08-20 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2017-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E 2 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.918401 NSLS-II 17-ID-1
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 3.15 50 99.9 0.125 16 18.6 25537
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 3.15 3.23 100 2.916 18
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 MOLECULAR REPLACEMENT THROUGHOUT 6C7K 3.15 49.58 24267 1269 99.93 0.23327 0.23155 0.2377 0.26579 0.2679 RANDOM 164.007
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] -8.58 -4.29 -8.58 27.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.001 r_dihedral_angle_3_deg 12.061 r_dihedral_angle_4_deg 11.922 r_long_range_B_refined 8.199 r_long_range_B_other 8.199 r_mcangle_it 5.941 r_mcangle_other 5.94 r_dihedral_angle_1_deg 4.894 r_scangle_other 4.81 r_mcbond_it 3.498
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.001 r_dihedral_angle_3_deg 12.061 r_dihedral_angle_4_deg 11.922 r_long_range_B_refined 8.199 r_long_range_B_other 8.199 r_mcangle_it 5.941 r_mcangle_other 5.94 r_dihedral_angle_1_deg 4.894 r_scangle_other 4.81 r_mcbond_it 3.498 r_mcbond_other 3.498 r_scbond_it 2.753 r_scbond_other 2.751 r_angle_refined_deg 0.968 r_angle_other_deg 0.79 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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 7536 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing