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Crystal structure of the zinc-beta-lactamase l1 from stenotrophomonas maltophilia (inhibitor 2)
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 7.75 281 1.8M ammonium sulfate, 0.1M Hepes pH 7.75, 1.5% V/V Peg 400, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.35 α = 90 b = 105.35 β = 90 c = 197.08 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 345 mm plate 2006-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591 1.54179
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 19.51 99.8 0.071 0.071 9.3 6.9 48803 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) 1.9 2 99.8 0.41 0.357 2.2 6.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1SML 1.9 19.51 48803 2613 99.86 0.18604 0.18427 0.21821 0.2039 RANDOM 19.42
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] 0.05 0.02 0.05 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.505 r_dihedral_angle_4_deg 20.571 r_dihedral_angle_3_deg 13.848 r_dihedral_angle_1_deg 6.281 r_sphericity_free 5.769 r_scangle_it 3.17 r_scbond_it 2.132 r_angle_refined_deg 1.495 r_mcangle_it 1.304 r_mcbond_it 0.843
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.505 r_dihedral_angle_4_deg 20.571 r_dihedral_angle_3_deg 13.848 r_dihedral_angle_1_deg 6.281 r_sphericity_free 5.769 r_scangle_it 3.17 r_scbond_it 2.132 r_angle_refined_deg 1.495 r_mcangle_it 1.304 r_mcbond_it 0.843 r_nbtor_refined 0.302 r_nbd_refined 0.276 r_symmetry_vdw_refined 0.218 r_symmetry_hbond_refined 0.156 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.093 r_metal_ion_refined 0.049 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4002 Nucleic Acid Atoms Solvent Atoms 469 Heterogen Atoms 65
Software Software Software Name Purpose XDS data scaling SCALA data scaling CCP4 model building REFMAC refinement XDS data reduction CCP4 data scaling CCP4 phasing