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OXA 10 class D beta-lactamase at pH 6.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E4D PDB entry 1e4d
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 ammonium sulfate, HEPES. Crystallization occured at pH 7.5. After obtaining the crystal, the pH was lowered to 6.0 for data collection., VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.53 51.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.755 α = 90 b = 82.52 β = 95.5 c = 101.791 γ = 90
Symmetry Space Group P 1 21 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 CCD MARRESEARCH 2000-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 33.77 97.8 0.085 0.085 9.7 2.5 84615 84615 22.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 2 94 0.404 0.404 3 2.3 11824
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB entry 1e4d 1.9 33.77 84560 84560 1693 97.6 0.18026 0.18026 0.17941 0.22234 0.2345 RANDOM 19.764
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] 0.25 -0.21 -0.13 -0.16
RMS Deviations Key Refinement Restraint Deviation p_scangle_it 5.208 p_scbond_it 3.278 p_mcangle_it 2.075 p_mcbond_it 1.181 p_bond_d 0.023 p_angle_d p_angle_deg p_planar_d p_hb_or_metal_coord p_plane_restr
RMS Deviations Key Refinement Restraint Deviation p_scangle_it 5.208 p_scbond_it 3.278 p_mcangle_it 2.075 p_mcbond_it 1.181 p_bond_d 0.023 p_angle_d p_angle_deg p_planar_d p_hb_or_metal_coord p_plane_restr p_chiral_restr p_singtor_nbd p_multtor_nbd p_xhyhbond_nbd p_xyhbond_nbd p_planar_tor p_staggered_tor p_orthonormal_tor p_transverse_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7663 Nucleic Acid Atoms Solvent Atoms 586 Heterogen Atoms 55
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement CCP4 data scaling