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The crystal structure of the RPGR RCC1-like domain in complex with PDE6D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JHN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.2M sodium chloride, 0.1M HEPES pH 7.5 and 12% (w/v) PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.52 51.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.83 α = 90 b = 58.78 β = 123.32 c = 92.11 γ = 90
Symmetry Space Group C 1 2 1
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 PILATUS 6M 2012-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97939 SLS X10SA
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 1.9 29.39 99.3 47164 47164 -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 1.9 2 99 0.525 3.43 3.2
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 4JHN 1.9 29.39 44805 2359 99.6 0.20074 0.19966 0.1991 0.22128 0.2194 RANDOM 26.379
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] 0.92 1.05 0.69 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.878 r_dihedral_angle_3_deg 12.306 r_dihedral_angle_4_deg 10.402 r_dihedral_angle_1_deg 4.617 r_angle_refined_deg 0.897 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3915 Nucleic Acid Atoms Solvent Atoms 413 Heterogen Atoms
Software Software Software Name Purpose PRO data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling