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Crystal structure of BJP-1, a subclass B3 metallo-beta-lactamase of Bradyrhizobium japonicum
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.1M Tris, 0.4M Na acetate, 40% PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.11 41.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.501 α = 78.92 b = 44.773 β = 89.51 c = 76.966 γ = 61.91
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2005-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.281302 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.4 38.576 91 87661
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.48 77.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 1.4 38.58 79603 79603 8006 100 0.1797 0.1797 0.17633 0.1752 0.21322 0.2123 RANDOM 16.071
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] -0.28 -0.05 -0.09 0.27 0.05 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.946 r_dihedral_angle_4_deg 13.595 r_dihedral_angle_3_deg 12.725 r_dihedral_angle_1_deg 5.41 r_sphericity_free 2.972 r_sphericity_bonded 2.912 r_scangle_it 2.681 r_scbond_it 1.82 r_mcangle_it 1.274 r_angle_refined_deg 1.163
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.946 r_dihedral_angle_4_deg 13.595 r_dihedral_angle_3_deg 12.725 r_dihedral_angle_1_deg 5.41 r_sphericity_free 2.972 r_sphericity_bonded 2.912 r_scangle_it 2.681 r_scbond_it 1.82 r_mcangle_it 1.274 r_angle_refined_deg 1.163 r_rigid_bond_restr 1.073 r_mcbond_it 0.823 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.187 r_xyhbond_nbd_refined 0.109 r_symmetry_hbond_refined 0.102 r_chiral_restr 0.073 r_metal_ion_refined 0.046 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4038 Nucleic Acid Atoms Solvent Atoms 713 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement ProDC data collection CCP4 data scaling SHELXD phasing SHARP phasing