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Variant W229D/F290W-19 of the last common ancestor of Gram-negative bacteria beta-lactamase class A (GNCA4)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UHU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 4.0 M Sodium formate, 100 mM Tris HCl pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.9 57.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.23 α = 90 b = 78.23 β = 90 c = 198.322 γ = 120
Symmetry Space Group P 65 2 2
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 6M 2019-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.38 47.31 99.98 0.0498 0.0515 0.0129 1 27.24 15.3 74330 15.91
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 1.38 1.43 100 0.6767 0.7146 0.2266 0.887 2.43 9.6
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 4UHU 1.38 47.31 1.36 74324 2000 99.99 0.1509 0.1505 0.1534 0.1659 0.1695 20.22
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 9.7032 f_angle_d 1.2742 f_chiral_restr 0.0964 f_bond_d 0.013 f_plane_restr 0.0091
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2021 Nucleic Acid Atoms Solvent Atoms 366 Heterogen Atoms 30
Software Software Software Name Purpose PHENIX refinement Coot model building EDNA data collection XDS data reduction Aimless data scaling PHASER phasing