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Crystal structure of the class D beta-lactamase OXA-13 in complex with meropenem
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other THE STARTING MODEL USED WAS THE ONE OF OXA-13
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 15-17% (W/V) PEG 4000, 0.1M SODIUM CACODYLATE PH 5.0-5.5, 0.2M LITHIUM SULFATE, PROTEIN 12-15 MG/ML
Crystal Properties Matthews coefficient Solvent content 2.9 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.34 α = 90 b = 112.3 β = 90 c = 124.98 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 CCD ADSC QUANTUM 4 2000-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2 30 97.7 0.092 15.5 6.5 43003 2.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.1 87.8 0.399 1.5 2.2
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 THE STARTING MODEL USED WAS THE ONE OF OXA-13 2 30 40758 2172 97.7 0.204 0.1946 0.257 0.2325 RANDOM 31.3
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 p_transverse_tor 30.5 p_staggered_tor 17.1 p_scangle_it 5.356 p_planar_tor 4.5 p_mcangle_it 3.981 p_scbond_it 3.738 p_mcbond_it 3.054 p_multtor_nbd 0.266 p_chiral_restr 0.183 p_singtor_nbd 0.183
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 30.5 p_staggered_tor 17.1 p_scangle_it 5.356 p_planar_tor 4.5 p_mcangle_it 3.981 p_scbond_it 3.738 p_mcbond_it 3.054 p_multtor_nbd 0.266 p_chiral_restr 0.183 p_singtor_nbd 0.183 p_planar_d 0.035 p_plane_restr 0.028 p_angle_d 0.025 p_bond_d 0.024 p_angle_deg p_hb_or_metal_coord p_xhyhbond_nbd p_xyhbond_nbd p_orthonormal_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3870 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing