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Crystal Structure of BJP-1 metallo beta-lactamase in complex with boric acid
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 0.2 M Lithium Suplhate, 30-35 % PEG400, 0.5 M sodium acetate, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.07 40.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.37 α = 78.8 b = 44.62 β = 89.13 c = 76.12 γ = 61.79
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 1.25 32.14 95.5 0.09 0.996 8.5 3.8 126849 2 5.7
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 1.25 1.32 95.48 0.488 0.976 3.4 3.8
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 3LVZ 1.25 32.14 120271 6575 95.48 0.13318 0.1316 0.1323 0.16209 0.1626 RANDOM 11.645
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 0.02 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.212 r_dihedral_angle_4_deg 14.744 r_sphericity_free 14.231 r_dihedral_angle_3_deg 11.608 r_dihedral_angle_1_deg 5.722 r_sphericity_bonded 3.166 r_long_range_B_refined 1.671 r_long_range_B_other 1.671 r_angle_refined_deg 1.535 r_rigid_bond_restr 1.401
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.212 r_dihedral_angle_4_deg 14.744 r_sphericity_free 14.231 r_dihedral_angle_3_deg 11.608 r_dihedral_angle_1_deg 5.722 r_sphericity_bonded 3.166 r_long_range_B_refined 1.671 r_long_range_B_other 1.671 r_angle_refined_deg 1.535 r_rigid_bond_restr 1.401 r_scangle_other 1.03 r_mcangle_it 0.953 r_mcangle_other 0.952 r_angle_other_deg 0.93 r_scbond_it 0.914 r_scbond_other 0.914 r_mcbond_it 0.798 r_mcbond_other 0.797 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 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 4119 Nucleic Acid Atoms Solvent Atoms 575 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing