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Crystal structures of a benzoate CoA ligase from Burkholderia xenovorans LB400
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MDF PDB ENTRY 1MDF
Crystallization Crystal Properties Matthews coefficient Solvent content 3.82 67.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.55 α = 70.06 b = 74.55 β = 79.95 c = 89.9 γ = 81.11
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 287 2007-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
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 1.84 39.41 92.2 0.08 7.5 3.5 141986 2
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 1.84 1.91 84.5 0.38 2.6 3.36
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 1MDF 1.84 36.66 134825 7152 92.3 0.223 0.221 0.2209 0.252 0.2524 RANDOM 27.05
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] 0.37 -0.12 -0.09 0.28 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.467 r_dihedral_angle_4_deg 19.94 r_dihedral_angle_3_deg 13.424 r_dihedral_angle_1_deg 6.214 r_scangle_it 3.67 r_scbond_it 2.431 r_angle_refined_deg 1.534 r_mcangle_it 1.441 r_mcbond_it 0.967 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.467 r_dihedral_angle_4_deg 19.94 r_dihedral_angle_3_deg 13.424 r_dihedral_angle_1_deg 6.214 r_scangle_it 3.67 r_scbond_it 2.431 r_angle_refined_deg 1.534 r_mcangle_it 1.441 r_mcbond_it 0.967 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.207 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.186 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.102 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 7520 Nucleic Acid Atoms Solvent Atoms 1062 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling MOLREP phasing