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E. coli GyrB 43-kDa N-terminal fragment in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EI1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293.15 10%(w/v) PEG20000, 20%(v/v) PEGMME550, 0.02M each carboxylic acid, 0.1M bicine/Trizma base pH 8.5, vapor diffusion, sitting drop, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 3.05 59.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.25 α = 90 b = 142.52 β = 90 c = 79.09 γ = 90
Symmetry Space Group C 2 2 21
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 2M 2012-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0000 SLS X06DA
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 2 75.03 88.2 0.068 22.15 30053 30053 -3 32.303
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.12 95.8 0.583 0.644 3.32
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) 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 1EI1 2 75.03 -3 30052 30052 2011 88.22 0.2102 0.2067 0.2142 0.2587 0.2585 RANDOM 28.952
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] -1.42 1.97 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.496 r_dihedral_angle_4_deg 19.323 r_dihedral_angle_3_deg 15.165 r_dihedral_angle_1_deg 6.29 r_angle_refined_deg 1.883 r_angle_other_deg 0.915 r_chiral_restr 0.12 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.496 r_dihedral_angle_4_deg 19.323 r_dihedral_angle_3_deg 15.165 r_dihedral_angle_1_deg 6.29 r_angle_refined_deg 1.883 r_angle_other_deg 0.915 r_chiral_restr 0.12 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2828 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 28
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction