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New refinement of the 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 30-35% PEG 4000, 0.5M sodium acetate, 5mM ZnCl2 pH 8.0-8.5, 0.1M TrisHCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.97 37.67
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 315r mirrors 2005-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.2813 ESRF ID29
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 1.4 38.58 91 0.06 7.1 3.7 87611 87611 1.6 14.05
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) 1.4 1.48 77.2 0.336 1.8 3.5 10821
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.4 32.24 2 79602 8006 100 0.16503 0.16217 0.19348 0.2328 RANDOM 9.088
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.152 r_dihedral_angle_4_deg 19.99 r_dihedral_angle_3_deg 12.124 r_dihedral_angle_1_deg 5.9 r_scangle_it 4.627 r_scbond_it 2.993 r_angle_refined_deg 2.204 r_mcangle_it 2.046 r_mcbond_it 1.273 r_angle_other_deg 1.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.152 r_dihedral_angle_4_deg 19.99 r_dihedral_angle_3_deg 12.124 r_dihedral_angle_1_deg 5.9 r_scangle_it 4.627 r_scbond_it 2.993 r_angle_refined_deg 2.204 r_mcangle_it 2.046 r_mcbond_it 1.273 r_angle_other_deg 1.093 r_mcbond_other 0.446 r_chiral_restr 0.131 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4109 Nucleic Acid Atoms Solvent Atoms 482 Heterogen Atoms 6
Software Software Software Name Purpose ADSC data collection SHARP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling