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Complex between a homodimer of Mycobacterium smegmatis MfpA and a single copy of the N-terminal 47 kDa fragment of the Mycobacterium smegmatis DNA Gyrase B subunit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZT3 6ZT3, 6ZT4 experimental model PDB 6ZT4 6ZT3, 6ZT4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 NULL
Crystal Properties Matthews coefficient Solvent content 3.06 59.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.545 α = 90 b = 59.38 β = 119.71 c = 141.217 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 EIGER X 16M 2019-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 2.2 75.32 100 0.048 0.052 0.02 0.996 14.4 6.9 55380 68.8
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 2.2 2.26 100 1.857 2.022 0.787 0.608 6.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6ZT3, 6ZT4 2.2 75.32 52549 2825 99.93 0.2102 0.208 0.2116 0.2515 0.251 RANDOM 70
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] 2.06 -1.17 5.46 -3.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.299 r_dihedral_angle_3_deg 16.068 r_dihedral_angle_4_deg 14.642 r_dihedral_angle_1_deg 6.577 r_angle_refined_deg 1.441 r_angle_other_deg 1.245 r_chiral_restr 0.057 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.299 r_dihedral_angle_3_deg 16.068 r_dihedral_angle_4_deg 14.642 r_dihedral_angle_1_deg 6.577 r_angle_refined_deg 1.441 r_angle_other_deg 1.245 r_chiral_restr 0.057 r_bond_refined_d 0.007 r_gen_planes_refined 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 5489 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 15
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction PHASER phasing