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Crystal structure of the zinc-beta-lactamase L1 from Stenotrophomonas maltophilia (mono zinc form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SML PDB ENTRY 1SML
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 280 AS, SOAKED CRYSTAL IN 5 ML DROP WITH CRYSTALLIZATION CONDITIONS AND 0.005 M EDTA FOR 30 MINUTES, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Crystal Properties Matthews coefficient Solvent content 2.54 51.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.22 α = 90 b = 104.22 β = 90 c = 195.74 γ = 120
Symmetry Space Group P 62 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 IMAGE PLATE MAR scanner 300 mm plate Xenocs multilayers 2006-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 1.8 19.74 97.7 0.096 0.096 5.7 6.6 57235 2
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) 1.8 1.9 97.7 0.468 0.372 1.6 5.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1SML 1.8 19.74 54307 2909 97.35 0.1735 0.17158 0.1713 0.20981 0.2102 RANDOM 15.145
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] 0.08 0.04 0.08 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.396 r_dihedral_angle_4_deg 15.221 r_dihedral_angle_3_deg 13.65 r_dihedral_angle_1_deg 7.605 r_scangle_it 3.343 r_scbond_it 2.091 r_angle_refined_deg 1.404 r_mcangle_it 1.211 r_mcbond_it 0.753 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.396 r_dihedral_angle_4_deg 15.221 r_dihedral_angle_3_deg 13.65 r_dihedral_angle_1_deg 7.605 r_scangle_it 3.343 r_scbond_it 2.091 r_angle_refined_deg 1.404 r_mcangle_it 1.211 r_mcbond_it 0.753 r_nbtor_refined 0.309 r_nbd_refined 0.291 r_symmetry_vdw_refined 0.211 r_symmetry_hbond_refined 0.185 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4049 Nucleic Acid Atoms Solvent Atoms 674 Heterogen Atoms 32
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling CCP4 model building REFMAC refinement XDS data reduction CCP4 data scaling CCP4 phasing