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Ultrahigh resolution structure of a class A beta-lactamase: On the mechanism and specificity of the extended-spectrum SHV-2 enzyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SHV PDB ENTRY 1SHV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 PEG 6000, HEPES, CYMAL-6, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.99 38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.74 α = 90 b = 55.58 β = 90 c = 83.3 γ = 90
Symmetry Space Group P 21 21 21
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 2001-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.948 CHESS F1
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 0.9 50 95.4 0.088 8.4 5 164255 164255
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 0.9 0.95 74.2 0.5 2.1 2.2 18796
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-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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1SHV 0.9 10 163646 163646 8189 95.8 0.1253 0.125 0.125 0.1304 0.15 0.1289 RANDOM 14.5
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 88 2020.18 2391.85
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.115 s_zero_chiral_vol 0.097 s_from_restr_planes 0.05 s_anti_bump_dis_restr 0.049 s_approx_iso_adps 0.041 s_angle_d 0.036 s_similar_adp_cmpnt 0.036 s_bond_d 0.017 s_rigid_bond_adp_cmpnt 0.006 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2204 Nucleic Acid Atoms Solvent Atoms 375 Heterogen Atoms 75
Software Software Software Name Purpose SHELXL-97 refinement SCALEPACK data scaling CNS refinement DENZO data reduction CNS phasing