☰ Navigation Tabs
Crystal Structure of a Beta-lactamase from Burkholderia ambifaria
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8D2Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 Berkeley B4: 1500 mM Ammonium sulfate, 100 mM Hepes free acid/ Sodium hydroxide pH 7.5 . BuamA.12746.a.B1.PW37793 at 23 mg/mL. plate 13822 E4 drop 1, Puck: OEP_08_10, Cryo: 20% PEG 200 + 80% crystallant
Crystal Properties Matthews coefficient Solvent content 3.7 66.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.007 α = 90 b = 76.443 β = 108.26 c = 105.058 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 PIXEL DECTRIS EIGER2 XE 9M 2024-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9786 NSLS-II 19-ID
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 3 49.88 99.9 0.152 0.165 0.063 0.997 8.7 6.8 22812
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 3 3.18 100 1.573 1.696 0.63 0.643 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3 43.27 1.34 22760 1145 99.68 0.2062 0.2041 0.2064 0.2464 0.2471
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 13.902 f_angle_d 0.765 f_chiral_restr 0.047 f_plane_restr 0.007 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4543 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 14
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction