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Crystal structure of RPE65 in complex with compound 16e and palmitate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RYX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10.5 281 30% PEG 400, 100 mM CAPS, pH 10.5, 500 mM ammonium sulfate, 10% v/v
Crystal Properties Matthews coefficient Solvent content 3.19 61.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 176.82 α = 90 b = 176.82 β = 90 c = 86.19 γ = 120
Symmetry Space Group P 65 2 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 ADSC HF-4M 2015-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979100 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.1 50 99.9 0.176 0.998 10.33 12.7 46592
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.23 99.8 2.338 0.399 1.09
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 4ryx 2.1 48.05 44331 2261 99.86 0.1793 0.1777 0.1877 0.2111 0.2251 RANDOM 41.965
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] -0.03 -0.02 -0.03 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.132 r_dihedral_angle_3_deg 11.536 r_dihedral_angle_1_deg 7.588 r_angle_refined_deg 1.073 r_angle_other_deg 0.37 r_chiral_restr 0.052 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4042 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling REFMAC phasing