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2.45A 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 293 150mM Bistris pH6.2, 11% PEG 5000 MME
Crystal Properties Matthews coefficient Solvent content 3.13 60.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.364 α = 90 b = 93.364 β = 90 c = 411.244 γ = 120
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 2010-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9795 ESRF ID23-1
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 2.45 40 95.9 0.084 8.2 2.8 70926 46.32
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 2.45 2.49 95.5 0.448 2.8 3495
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 2.45 39.78 70923 2860 95.88 0.178 0.1766 0.1762 0.211 0.2106 RANDOM 37.83
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] 0.9203 0.9203 -1.8407
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.37 t_omega_torsion 2.67 t_angle_deg 1.03 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.37 t_omega_torsion 2.67 t_angle_deg 1.03 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle 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 10611 Nucleic Acid Atoms 801 Solvent Atoms 770 Heterogen Atoms 48
Software Software Software Name Purpose SCALEPACK data scaling BUSTER-TNT refinement PDB_EXTRACT data extraction PHENIX phasing DENZO data reduction