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The crystal structure of a beta-lactamase from Chitinophaga pinensis DSM 2588
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5G58
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 296 0.2 M Magnesium Chloride,
0.1 M MES:NaOH,
25% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.1 41.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.702 α = 90 b = 76.313 β = 90 c = 89.376 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 PIXEL DECTRIS PILATUS3 S 6M 2018-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.28 50 97.7 0.099 0.121 0.067 23.1 3 127393 -3 15.83
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.28 1.3 97.2 0.771 0.961 0.563 0.457 1.1 2.5
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5G58 1.29 38.48 1.34 127043 6346 97.39 0.1619 0.1606 0.1619 0.1863 0.1876 random 21.15
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 16.4476 f_angle_d 0.8471 f_chiral_restr 0.0746 f_bond_d 0.005 f_plane_restr 0.0044
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4162 Nucleic Acid Atoms Solvent Atoms 539 Heterogen Atoms 35
Software Software Software Name Purpose SBC-Collect data collection PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing