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2.60A BINARY COMPLEX OF S.AUREUS GYRASE with UNCLEAVED DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CDR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5.9 293 Complex made as 13uls of protein (24mgs/ml in 20mM HEPES, 100mM Na2SO4, 5mM MnCl2, pH 7.0) + 1.5ul of 40mM MgCl2 in 15% glycerol, 3ul of DNA (2mM duplex = 4mM monomer in water) + 2uls of 50% glycerol. Crystallisation buffer 9% PEG 5000mme, 80mM BisTris 5.9. 0.7ul complex + 0.8ul crystallisation buffer. CRYO:20% glycerol + 10.8% PEG 5000MME, 60mM BisTris 5.9,.
Crystal Properties Matthews coefficient Solvent content 2.66 53.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.28 α = 90 b = 124.64 β = 95.65 c = 155.24 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 PIXEL DECTRIS PILATUS 6M 2015-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9762 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.6 20 99.1 0.102 0.994 9.3 4.5 107487 68.55
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 99.3 1.02 0.527 1.3 4.6
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 5CDR 2.6 19.91 107487 5247 99.16 0.2014 0.1996 0.2062 0.2362 0.2426 RANDOM 63
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] -5.8475 5.481 -0.7499 6.5974
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.34 t_omega_torsion 2.52 t_angle_deg 1.03 t_bond_d 0.009 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 18.34 t_omega_torsion 2.52 t_angle_deg 1.03 t_bond_d 0.009 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 21067 Nucleic Acid Atoms 1567 Solvent Atoms 468 Heterogen Atoms 78
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing