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Crystal structure of Streptococcus pyogenes macrodomain in complex with ADP-ribose
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 293.15 100 mM sodium cocadylate [pH 6.5], 27% (w/v) PEG2000MME
Crystal Properties Matthews coefficient Solvent content 1.97 37.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.704 α = 90 b = 41.704 β = 90 c = 137.895 γ = 90
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 PILATUS3 6M 2015-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 1.2822 Diamond I03
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 1.87 68.95 99.8 0.998 12.6 6.6 19406
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 1.87 1.91 97.2 0.536 2.7 4.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.87 41.704 19352 1005 99.814 0.155 0.1529 0.1587 0.201 0.205 26.749
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] -0.903 -0.903 1.806
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 19.904 r_dihedral_angle_3_deg 16.988 r_dihedral_angle_6_deg 15.989 r_dihedral_angle_2_deg 15.655 r_lrange_it 6.936 r_lrange_other 6.911 r_dihedral_angle_1_deg 6.216 r_scangle_it 5.177 r_scangle_other 5.176 r_scbond_it 3.428
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 19.904 r_dihedral_angle_3_deg 16.988 r_dihedral_angle_6_deg 15.989 r_dihedral_angle_2_deg 15.655 r_lrange_it 6.936 r_lrange_other 6.911 r_dihedral_angle_1_deg 6.216 r_scangle_it 5.177 r_scangle_other 5.176 r_scbond_it 3.428 r_scbond_other 3.427 r_mcangle_other 3.325 r_mcangle_it 3.324 r_mcbond_it 2.206 r_mcbond_other 2.206 r_angle_refined_deg 1.644 r_angle_other_deg 0.56 r_dihedral_angle_other_2_deg 0.548 r_symmetry_xyhbond_nbd_refined 0.265 r_nbd_other 0.23 r_nbd_refined 0.219 r_symmetry_nbd_refined 0.207 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.15 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.078 r_symmetry_xyhbond_nbd_other 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1993 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing