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Crystal structure of Methanobrevibacter oralis macrodomain in complex with Asn-ADPr
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 5 mM zinc acetate, 9% (w/v) PEG8000, 100 mM sodium cocadylate pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.94 58.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.146 α = 90 b = 110.443 β = 119.559 c = 104.61 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 2017-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 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 2.359 69.955 99.9 0.993 7.3 3.1 42263
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 2.36 2.42 0.494 0.9
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 2.359 69.955 42051 1951 99.151 0.216 0.2134 0.2199 0.2607 0.2626 58.761
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] 0.475 0.736 -3.208 1.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.358 r_dihedral_angle_other_3_deg 16.985 r_dihedral_angle_6_deg 16.049 r_dihedral_angle_2_deg 10.207 r_lrange_other 8.491 r_lrange_it 8.483 r_dihedral_angle_1_deg 7.431 r_scangle_it 5.758 r_scangle_other 5.758 r_mcangle_it 4.577
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.358 r_dihedral_angle_other_3_deg 16.985 r_dihedral_angle_6_deg 16.049 r_dihedral_angle_2_deg 10.207 r_lrange_other 8.491 r_lrange_it 8.483 r_dihedral_angle_1_deg 7.431 r_scangle_it 5.758 r_scangle_other 5.758 r_mcangle_it 4.577 r_mcangle_other 4.577 r_scbond_other 3.948 r_scbond_it 3.945 r_mcbond_it 2.927 r_mcbond_other 2.893 r_angle_refined_deg 2.211 r_angle_other_deg 0.683 r_nbd_other 0.45 r_symmetry_xyhbond_nbd_refined 0.291 r_nbd_refined 0.227 r_symmetry_nbd_refined 0.218 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.16 r_symmetry_metal_ion_refined 0.098 r_ncsr_local_group_3 0.095 r_chiral_restr 0.093 r_ncsr_local_group_2 0.093 r_ncsr_local_group_1 0.091 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.015 r_symmetry_xyhbond_nbd_other 0.014 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 6225 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 185
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing