☰ Navigation Tabs
Crystal structure of PenI beta-lactamase from Burkholderia pseudomallei at pH7.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W4O the structure of PenI at pH9.5(now diposited together with this)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 25% PEG8000, 0.1M HEPES, 0.1M ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 1.94 36.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.354 α = 90 b = 52.721 β = 92.48 c = 50.523 γ = 90
Symmetry Space Group P 1 21 1
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 270 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.000 Photon Factory AR-NE3A
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 1.05 50 97.8 0.092 13.6 3.82 98393
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 (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 FREE R the structure of PenI at pH9.5(now diposited together with this) 1.05 15 95315 95315 2120 94.5 0.1345 0.1345 0.1391 0.1602 0.1566 RANDOM
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 28 1932.6 2198.2
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.096 s_approx_iso_adps 0.094 s_zero_chiral_vol 0.081 s_from_restr_planes 0.0333 s_angle_d 0.029 s_anti_bump_dis_restr 0.026 s_similar_adp_cmpnt 0.023 s_bond_d 0.014 s_rigid_bond_adp_cmpnt 0.005 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1990 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 23
Software Software Software Name Purpose HKL-2000 data collection PHENIX model building SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing