☰ Navigation Tabs
Variant W229D/F290W-12 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 5FQK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 COUNTER-DIFFUSION 4 293 5.0 M Sodium formate, 100 mM AcNa pH 4.0
Crystal Properties Matthews coefficient Solvent content 3.9 68.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.314 α = 90 b = 148.228 β = 90 c = 245.962 γ = 90
Symmetry Space Group I 2 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 0.979 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 2 71.74 98.99 0.103 0.118 0.056 0.993 11.89 4.5 95172 28.62
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 2 2.07 98.87 0.678 0.771 0.3612 0.81 2.63 4.5
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5FQK 2 71.74 1.34 94616 4769 99 0.213 0.2119 0.2352 0.2358 38.25
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 4.8421 f_angle_d 0.5897 f_chiral_restr 0.0374 f_plane_restr 0.0034 f_bond_d 0.0024
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6023 Nucleic Acid Atoms Solvent Atoms 422 Heterogen Atoms 59
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data reduction Aimless data scaling PHASER phasing