☰ Navigation Tabs
Crystal Structure of PenA39 beta-Lactamase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W4Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 294 250 microL reservoir (30% MPD, 12.5% polyethylene glycol 1500, 0.1 M Sodium Acetate buffer pH 4.5) with a 4 microL hanging drop (7.5 mg/ml protein, 15% MPD, 6.3% PEG 1500, 0.05 M sodium acetate buffer pH 4.5), Loop-mounted crystals were flash-cooled without additional cryoprotectant and kept at 100 K with a nitrogen gas stream.
Crystal Properties Matthews coefficient Solvent content 1.95 36.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.519 α = 90 b = 65.519 β = 90 c = 51.421 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2018-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
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 38.1 99.7 0.027 32 5.4 76919 10.36
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22 96.4 0.264 5.9 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3W4Q 1.2 38.1 1.57 76895 3845 99.75 0.1261 0.1252 0.1277 0.144 0.1448 14.24
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.6723 f_angle_d 0.9117 f_chiral_restr 0.0761 f_plane_restr 0.0053 f_bond_d 0.0051
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1993 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing