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3.06A COMPLEX OF S.AUREUS GYRASE with imidazopyrazinone T1 AND DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CDQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.2 293 8% PEG 5000 MME, 90 mM bis-tris pH 6.2
Crystal Properties Matthews coefficient Solvent content 2.74 55.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.34 α = 90 b = 171.71 β = 102.86 c = 124.87 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 PILATUS3 6M 2014-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.06 60 98.6 0.994 8.3 3.4 67466
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.06 3.14 99.9 0.654 1.6 3.4
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 FOURIER SYNTHESIS THROUGHOUT 5CDQ 3.06 59.9 64115 3323 98.63 0.19678 0.19481 0.1973 0.2344 0.2379 RANDOM 97.244
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] 0.46 2.86 -8.04 5.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.267 r_dihedral_angle_4_deg 18.588 r_dihedral_angle_3_deg 17.328 r_long_range_B_refined 14.413 r_mcangle_it 7.408 r_scbond_it 5.462 r_mcbond_it 4.682 r_dihedral_angle_1_deg 4.048 r_angle_refined_deg 1.691 r_chiral_restr 0.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.267 r_dihedral_angle_4_deg 18.588 r_dihedral_angle_3_deg 17.328 r_long_range_B_refined 14.413 r_mcangle_it 7.408 r_scbond_it 5.462 r_mcbond_it 4.682 r_dihedral_angle_1_deg 4.048 r_angle_refined_deg 1.691 r_chiral_restr 0.144 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19206 Nucleic Acid Atoms 1558 Solvent Atoms 55 Heterogen Atoms 164
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHENIX phasing