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Crystal structure of a 59 kDa fragment of topoisomerase IV subunit A (GrlA) from Staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AB4 PDB entry 1AB4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 50 mM tris.HCl, pH 8.5, 200 mM NaCl, 12-16% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.67 53.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.458 α = 90 b = 171.885 β = 90 c = 87.892 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 225 mm CCD mirrors 2006-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.8 88 99.3 0.084 0.084 13.5 3.6 16226 16113 1 1 78.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 98.6 0.425 0.425 3.1 3.5 2289
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 PDB entry 1AB4 2.8 19.64 1 1 15735 15239 803 99.1 0.23661 0.23414 0.31 0.28342 0.3458 RANDOM 24.01
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.353 r_dihedral_angle_3_deg 19.422 r_dihedral_angle_4_deg 17.759 r_dihedral_angle_1_deg 5.557 r_scangle_it 1.682 r_angle_refined_deg 1.215 r_scbond_it 1.036 r_mcangle_it 0.772 r_mcbond_it 0.445 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.353 r_dihedral_angle_3_deg 19.422 r_dihedral_angle_4_deg 17.759 r_dihedral_angle_1_deg 5.557 r_scangle_it 1.682 r_angle_refined_deg 1.215 r_scbond_it 1.036 r_mcangle_it 0.772 r_mcbond_it 0.445 r_nbtor_refined 0.307 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.143 r_symmetry_hbond_refined 0.13 r_symmetry_vdw_refined 0.119 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3528 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing