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VIM-2, a Zn-beta-lactamase from Pseudomonas aeruginosa with an oxidized Cys (cysteinesulfonic)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BVT PDB-ENTRY 1BVT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 30% PEG8K, 0.2M Na acetate, 0.1M NaCac./Cac.acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.02 38.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.18 α = 90 b = 78.03 β = 90 c = 80.13 γ = 90
Symmetry Space Group I 2 2 2
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 4 2000-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97929 ESRF BM14
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 1.78 30 69 13 34075 20045 3 16.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.78 1.85 49.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 1BVT 2.2 21.45 19877 10190 994 94 0.2088 0.245 0.2506 0.2537 random 22.2
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] 2.21 2.64 -4.85
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25 c_improper_angle_d 1.5 c_angle_deg 1.3 c_mcangle_it 1.04 c_scangle_it 0.96 c_scbond_it 0.6 c_mcbond_it 0.58 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1736 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 10
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement