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Crystal structure of PenA beta-lactamase from Burkholderia multivorans at pH4.2
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 4.2 298 20% PEG8000, 0.1M phosphate/citrate, 0.2M sodium chloride, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.16 43.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.017 α = 90 b = 69.91 β = 89.996 c = 84.35 γ = 90
Symmetry Space Group C 1 2 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 2012-03-10 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 1.2 50 95.5 0.039 31.6 4.04 208965
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) 1.2 15 202528 202528 6408 92.5 0.1322 0.1322 0.1374 0.1749 0.1725 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 52 5558 6651
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.106 s_non_zero_chiral_vol 0.08 s_zero_chiral_vol 0.074 s_anti_bump_dis_restr 0.035 s_from_restr_planes 0.0317 s_angle_d 0.031 s_similar_adp_cmpnt 0.023 s_bond_d 0.013 s_rigid_bond_adp_cmpnt 0.004 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5724 Nucleic Acid Atoms Solvent Atoms 929 Heterogen Atoms
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