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Crystal structure of Methanobrevibacter oralis macrodomain in complex with ADPr in open conformation
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 293.15 200 mM sodium fluoride, 100 mM BisTris propane [pH 7.5], 20% (w/v) PEG3350< 1 M potassium sodium tartrate tetrahydrate
Crystal Properties Matthews coefficient Solvent content 2.51 51.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.986 α = 90 b = 58.101 β = 117.664 c = 76.269 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 PILATUS3 6M 2016-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966000 ESRF MASSIF-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 1.66 67.39 98.5 0.999 18.7 6 68604
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 1.66 1.69 0.873 3.3
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 1.66 67.39 68583 3322 98.34 0.194 0.1921 0.2009 0.2319 0.2367 24.098
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] -1.216 0.871 -1.658 1.265
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.633 r_dihedral_angle_3_deg 14.805 r_dihedral_angle_2_deg 6.737 r_dihedral_angle_1_deg 6.541 r_lrange_it 5.7 r_lrange_other 5.533 r_scangle_it 3.059 r_scangle_other 3.059 r_chiral_restr_other 2.317 r_mcangle_other 2.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.633 r_dihedral_angle_3_deg 14.805 r_dihedral_angle_2_deg 6.737 r_dihedral_angle_1_deg 6.541 r_lrange_it 5.7 r_lrange_other 5.533 r_scangle_it 3.059 r_scangle_other 3.059 r_chiral_restr_other 2.317 r_mcangle_other 2.3 r_mcangle_it 2.299 r_scbond_it 1.984 r_scbond_other 1.983 r_angle_refined_deg 1.662 r_mcbond_it 1.589 r_mcbond_other 1.582 r_angle_other_deg 0.737 r_symmetry_xyhbond_nbd_refined 0.225 r_nbd_refined 0.201 r_nbtor_refined 0.166 r_symmetry_nbd_other 0.158 r_xyhbond_nbd_refined 0.143 r_symmetry_nbd_refined 0.14 r_nbd_other 0.14 r_chiral_restr 0.122 r_metal_ion_refined 0.113 r_symmetry_nbtor_other 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4141 Nucleic Acid Atoms Solvent Atoms 622 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing