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Crystal Structure of GyraseA N-terminal at 2.43A Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RKS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG 3500, Tris
Crystal Properties Matthews coefficient Solvent content 3.41 63.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.781 α = 90 b = 154.781 β = 90 c = 108.258 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 PIXEL DECTRIS EIGER2 X 9M 2023-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8731 ESRF ID23-2
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 2.42 134.04 99.1 0.993 8.8 10.1 55446
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 2.42 2.49 0.375
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.428 45.93 55206 2005 99.062 0.201 0.1993 0.1996 0.2348 0.2396 51.717
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] 0.037 0.018 0.037 -0.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.387 r_dihedral_angle_6_deg 15.694 r_dihedral_angle_2_deg 12.649 r_dihedral_angle_1_deg 5.227 r_rigid_bond_restr 4.527 r_angle_refined_deg 1.29 r_angle_other_deg 0.623 r_symmetry_xyhbond_nbd_refined 0.397 r_xyhbond_nbd_other 0.386 r_symmetry_nbd_refined 0.285
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.387 r_dihedral_angle_6_deg 15.694 r_dihedral_angle_2_deg 12.649 r_dihedral_angle_1_deg 5.227 r_rigid_bond_restr 4.527 r_angle_refined_deg 1.29 r_angle_other_deg 0.623 r_symmetry_xyhbond_nbd_refined 0.397 r_xyhbond_nbd_other 0.386 r_symmetry_nbd_refined 0.285 r_nbd_other 0.26 r_symmetry_nbd_other 0.221 r_nbd_refined 0.202 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.167 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.06 r_symmetry_xyhbond_nbd_other 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_lrange_it r_lrange_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7702 Nucleic Acid Atoms Solvent Atoms 627 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing MxCuBE data collection Coot model building