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Crystal structure of N-terminal domain of GyrA with the antibiotic simocyclinone D8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AB4 PDB ENTRY 1AB4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 6% (W/V) PEG 8000, 30% (V/V) GLYCEROL IN 100 MM TRIS-HCL PH 8.5.
Crystal Properties Matthews coefficient Solvent content 4.18 70.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.91 α = 90 b = 153.09 β = 90 c = 177.7 γ = 90
Symmetry Space Group I 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate MIRRORS 2007-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
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 2.62 27.47 99.8 0.09 14 5.1 58959 -9 46.8
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 2.62 2.76 99.8 0.51 3.3 4.8
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 PDB ENTRY 1AB4 2.62 27.47 55953 2967 99.73 0.20399 0.20203 0.2037 0.24118 0.2423 RANDOM 52.1
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] 0.48 0.02 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.238 r_dihedral_angle_4_deg 19.678 r_dihedral_angle_3_deg 19.405 r_dihedral_angle_1_deg 6.429 r_scangle_it 4.204 r_scbond_it 2.469 r_angle_refined_deg 1.837 r_mcangle_it 1.362 r_mcbond_it 0.696 r_chiral_restr 0.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.238 r_dihedral_angle_4_deg 19.678 r_dihedral_angle_3_deg 19.405 r_dihedral_angle_1_deg 6.429 r_scangle_it 4.204 r_scbond_it 2.469 r_angle_refined_deg 1.837 r_mcangle_it 1.362 r_mcbond_it 0.696 r_chiral_restr 0.196 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 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_other r_long_range_B_refined 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 7721 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing