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M. smegmatis antimutator protein MutT2 in complex with dCMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZRC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 292 0.1 M Imidazole pH 6.5, 1.0 M Sodium acetate trihydrate
Cryo: 5% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 1.96 35.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.08 α = 90 b = 59.36 β = 90 c = 31.36 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 CCD MARMOSAIC 300 mm CCD 2014-12-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.9762 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.3 22.08 97.9 0.085 11.5 7.7 30397
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.37 96.2 0.98 7.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5ZRC 1.3 22.08 28630 1533 96.92 0.14451 0.14232 0.1442 0.18365 0.186 RANDOM 18.793
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] 1.13 -0.53 -0.6
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 55.838 r_dihedral_angle_2_deg 29.698 r_sphericity_bonded 20.88 r_rigid_bond_restr 14.705 r_long_range_B_refined 14.101 r_dihedral_angle_4_deg 13.314 r_dihedral_angle_3_deg 11.163 r_long_range_B_other 10.991 r_dihedral_angle_1_deg 7.168 r_scangle_other 5.3
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 55.838 r_dihedral_angle_2_deg 29.698 r_sphericity_bonded 20.88 r_rigid_bond_restr 14.705 r_long_range_B_refined 14.101 r_dihedral_angle_4_deg 13.314 r_dihedral_angle_3_deg 11.163 r_long_range_B_other 10.991 r_dihedral_angle_1_deg 7.168 r_scangle_other 5.3 r_scbond_it 4.721 r_scbond_other 4.718 r_mcangle_other 3.902 r_mcangle_it 3.883 r_mcbond_it 3.058 r_mcbond_other 2.908 r_angle_refined_deg 1.618 r_angle_other_deg 0.858 r_chiral_restr 0.112 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_gen_planes_other 0.004 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 932 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing