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Structure of RPE65: P6522 crystal form grown in ammonium phosphate solution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F3A PDB ENTRY 4F3A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 281 1 M ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties Matthews coefficient Solvent content 3.26 62.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.497 α = 90 b = 178.497 β = 90 c = 86.642 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 CCD ADSC QUANTUM 315 2010-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.97949 NSLS X29A
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 0.108 12.1 4.1 14356 14356 -3 -3
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 3.35 98.6 0.495 2.78 4.1
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 4F3A 3.15 48.44 13635 13635 717 99.1 0.21658 0.215 0.1876 0.24707 0.239 RANDOM 63.122
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] 2.03 1.02 2.03 -3.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.604 r_dihedral_angle_4_deg 13.263 r_dihedral_angle_3_deg 13.215 r_dihedral_angle_1_deg 5.899 r_angle_refined_deg 1.006 r_angle_other_deg 0.648 r_chiral_restr 0.058 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.604 r_dihedral_angle_4_deg 13.263 r_dihedral_angle_3_deg 13.215 r_dihedral_angle_1_deg 5.899 r_angle_refined_deg 1.006 r_angle_other_deg 0.648 r_chiral_restr 0.058 r_bond_refined_d 0.005 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 4213 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 6
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction