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Crystal Structure of the WD repeat-containing protein 61
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FRX pdb entry 3frx
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 Mix 0.5uL precipitant (6% PEG20000, 8% PEG-MME550, 0.2M calcium acetate), 0.5uL protein stock solution (11 mg/mL protein), 0.2 uL additive (5% w/v polyvinylpyrrolidine K15), vapor diffusion, sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.43 49.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.544 α = 114.34 b = 72.922 β = 96.44 c = 81.514 γ = 90.12
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 2010-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97934 APS 19-ID
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 2.3 40 97.8 0.106 9.89 1.9 58481
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) 2.3 2.34 96 0.865 1.05 1.8 2898
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. Change of flag assignment was followed by slow-cool simulated annealing (from temperature = 5000.0, phenix). pdb entry 3frx 2.3 30 58241 2000 100 0.245 0.244 0.2439 0.2766 0.2783 phenix.reflection_file_converter --use-lattice-symmetry-in-r-free-flag-generation 29.377
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] -2.228 -0.256 -0.235 -0.925 0.491 3.505
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.43 r_dihedral_angle_3_deg 13.38 r_dihedral_angle_4_deg 13.022 r_dihedral_angle_1_deg 6.18 r_scangle_it 1.213 r_angle_refined_deg 1.1 r_angle_other_deg 0.812 r_scbond_it 0.79 r_mcangle_it 0.456 r_mcbond_it 0.249
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.43 r_dihedral_angle_3_deg 13.38 r_dihedral_angle_4_deg 13.022 r_dihedral_angle_1_deg 6.18 r_scangle_it 1.213 r_angle_refined_deg 1.1 r_angle_other_deg 0.812 r_scbond_it 0.79 r_mcangle_it 0.456 r_mcbond_it 0.249 r_chiral_restr 0.066 r_mcbond_other 0.066 r_bond_refined_d 0.011 r_gen_planes_refined 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 8828 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 35
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling