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N-terminal 47 kDa fragment of the Mycobacterium smegmatis DNA Gyrase B subunit complexed with ADPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZKB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 NULL
Crystal Properties Matthews coefficient Solvent content 2.38 48.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.985 α = 90 b = 76.985 β = 90 c = 261.476 γ = 120
Symmetry Space Group P 61 2 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 EIGER X 16M 2019-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.56 65.37 100 0.141 0.143 0.023 1 16.7 38.8 66509 19.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.56 1.59 100 2.486 2.518 0.399 0.845 39.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3ZKB 1.56 64.69 63082 3287 99.99 0.1493 0.1469 0.1939 0.1839 RANDOM 23.46
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] -1.84 -0.92 -1.84 5.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.84 r_dihedral_angle_4_deg 18.378 r_dihedral_angle_3_deg 15.125 r_dihedral_angle_1_deg 6.279 r_rigid_bond_restr 3.043 r_angle_other_deg 1.44 r_angle_refined_deg 1.368 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_bond_other_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.84 r_dihedral_angle_4_deg 18.378 r_dihedral_angle_3_deg 15.125 r_dihedral_angle_1_deg 6.279 r_rigid_bond_restr 3.043 r_angle_other_deg 1.44 r_angle_refined_deg 1.368 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_bond_other_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3033 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 57
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction PHASER phasing