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Crystal structure of Methanobrevibacter oralis 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 46.8 mM MES monohydrate, 53.2 mM imidazole, 20% (v/v) ethylene glycol, 10% (w/v) PEG8000
Crystal Properties Matthews coefficient Solvent content 2.53 51.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.32 α = 90 b = 146.609 β = 90 c = 58.295 γ = 90
Symmetry Space Group P 21 21 2
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 2017-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 1.28229 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 2.059 146.39 100 0.992 6.7 12.1 38093
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 2.059 2.11 0.457 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 2.059 73.412 37960 1799 99.478 0.195 0.1927 0.2007 0.2437 0.2475 45.758
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] -1.076 1.585 -0.509
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.11 r_dihedral_angle_6_deg 15.447 r_lrange_it 8.276 r_lrange_other 8.275 r_dihedral_angle_2_deg 7.77 r_dihedral_angle_1_deg 6.413 r_scangle_it 6.243 r_scangle_other 6.243 r_mcangle_it 4.373 r_mcangle_other 4.372
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.11 r_dihedral_angle_6_deg 15.447 r_lrange_it 8.276 r_lrange_other 8.275 r_dihedral_angle_2_deg 7.77 r_dihedral_angle_1_deg 6.413 r_scangle_it 6.243 r_scangle_other 6.243 r_mcangle_it 4.373 r_mcangle_other 4.372 r_scbond_it 4.227 r_scbond_other 4.167 r_mcbond_it 3.008 r_mcbond_other 3.007 r_angle_refined_deg 1.729 r_angle_other_deg 0.58 r_symmetry_nbd_refined 0.329 r_symmetry_xyhbond_nbd_refined 0.271 r_nbd_refined 0.23 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.181 r_nbd_other 0.179 r_metal_ion_refined 0.101 r_ncsr_local_group_1 0.091 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_chiral_restr_other 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4124 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing