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2.8A structure of etoposide with S.aureus DNA gyrase and DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XCS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.2 293 150mM Bis Tris pH6.2, 11% PEG 5000 MME
Crystal Properties Matthews coefficient Solvent content 2.84 56.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.782 α = 90 b = 170.081 β = 102.27 c = 124.54 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 315 2011-01-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.950 Diamond I03
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 2.8 40 96.6 0.103 10.1 3 87189 74.37
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.85 96.1 0.399 2.9 4312
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 2XCS 2.79 39.35 87157 3484 96.13 0.2143 0.2132 0.2294 0.242 0.2655 RANDOM 77.78
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] -7.0169 -0.722 24.5222 -17.5053
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.12 t_omega_torsion 1.96 t_angle_deg 0.98 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.12 t_omega_torsion 1.96 t_angle_deg 0.98 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20783 Nucleic Acid Atoms 1589 Solvent Atoms 412 Heterogen Atoms 202
Software Software Software Name Purpose BUSTER refinement SCALEPACK data scaling PDB_EXTRACT data extraction DENZO data reduction PHASER phasing