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The DNA Gyrase B ATP binding domain of Enterococcus faecalis in complex with a small molecule inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GEE PDB ENTRY 4GEE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 25% (W/V) PEG 1500, 3% (V/V) T-BUTANOL, 20% (W/V) GLYCEROL, 20 MM CITRATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.45 α = 90 b = 58.35 β = 90 c = 65.55 γ = 90
Symmetry Space Group P 21 21 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 CCD NOIR-1 2013-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 0.976200 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 43.58 99.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.38 97.6
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 PDB ENTRY 4GEE 1.3 43.58 49219 2648 99.19 0.17911 0.17821 0.1781 0.19614 0.1961 RANDOM 12.331
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] -0.34 0.57 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.264 r_dihedral_angle_4_deg 10.847 r_dihedral_angle_3_deg 10.012 r_dihedral_angle_1_deg 5.324 r_angle_refined_deg 1.417 r_chiral_restr 0.076 r_gen_planes_refined 0.008 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1503 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement