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Crystal structure of the subclass B3 metallo-beta-lactamase BJP-1 in complex with acetate anion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LVZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 295 BJP-1 (10 mg mL-1 in 0.1 M Tris-HCl pH 8.5 and 5 mM zinc(II) chloride) mixed with precipitant (0.2 M lithium sulfate, 30-35 % PEG4000, 0.5 M sodium acetate pH 8.5)
Crystal Properties Matthews coefficient Solvent content 1.93 36.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.31 α = 78.88 b = 44.64 β = 89.41 c = 75.91 γ = 61.99
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 MARMOSAIC 225 mm CCD 2008-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.18 34.68 94.5 0.06 0.997 9.8 4 148959 2 6.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.18 1.24 92.2 0.387 0.806 3 4
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 3LVZ 1.18 34.68 141256 7703 94.5 0.122 0.12071 0.1205 0.14601 0.1456 RANDOM 14.912
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] -0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.073 r_sphericity_free 24.653 r_dihedral_angle_4_deg 20.02 r_sphericity_bonded 11.876 r_dihedral_angle_3_deg 11.437 r_dihedral_angle_1_deg 5.716 r_rigid_bond_restr 3.428 r_long_range_B_refined 3.06 r_long_range_B_other 2.714 r_scangle_other 2.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.073 r_sphericity_free 24.653 r_dihedral_angle_4_deg 20.02 r_sphericity_bonded 11.876 r_dihedral_angle_3_deg 11.437 r_dihedral_angle_1_deg 5.716 r_rigid_bond_restr 3.428 r_long_range_B_refined 3.06 r_long_range_B_other 2.714 r_scangle_other 2.154 r_angle_other_deg 2.067 r_mcangle_other 1.719 r_mcangle_it 1.718 r_scbond_it 1.62 r_scbond_other 1.62 r_mcbond_it 1.487 r_mcbond_other 1.484 r_angle_refined_deg 1.458 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d 0.002 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4100 Nucleic Acid Atoms Solvent Atoms 627 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing