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Crystal structure of Staphylococcus aureus macrodomain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KIV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 18.5% (v/v) PEG400, 12.5% (v/v) 1-propanol, 4% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 2.11 41.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.19 α = 90 b = 139.4 β = 93.76 c = 49.19 γ = 90
Symmetry Space Group P 1 21 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 2M 2014-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92000 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.94 49.084 97.9 0.999 18.8 3.4 39007
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 1.99 0.702 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.94 49.084 38974 1911 97.772 0.166 0.1635 0.2132 0.2099 33.165
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] -0.806 -0.056 0.14 0.668
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 17.169 r_dihedral_angle_3_deg 16.923 r_dihedral_angle_6_deg 16.585 r_dihedral_angle_2_deg 9.48 r_lrange_it 8.945 r_lrange_other 8.917 r_scangle_it 6.802 r_scangle_other 6.801 r_dihedral_angle_1_deg 6.277 r_mcangle_it 4.808
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 17.169 r_dihedral_angle_3_deg 16.923 r_dihedral_angle_6_deg 16.585 r_dihedral_angle_2_deg 9.48 r_lrange_it 8.945 r_lrange_other 8.917 r_scangle_it 6.802 r_scangle_other 6.801 r_dihedral_angle_1_deg 6.277 r_mcangle_it 4.808 r_mcangle_other 4.808 r_scbond_other 4.462 r_scbond_it 4.461 r_mcbond_it 3.359 r_mcbond_other 3.349 r_angle_refined_deg 1.699 r_angle_other_deg 0.596 r_symmetry_nbd_refined 0.293 r_nbd_other 0.23 r_nbd_refined 0.221 r_symmetry_xyhbond_nbd_refined 0.189 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.175 r_symmetry_xyhbond_nbd_other 0.095 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.08 r_ncsr_local_group_1 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4282 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing