☰ Navigation Tabs
Crystal Structure of the Zinc-Beta-Lactamase L1 from Stenotrophomonas Maltophilia (Inhibitor 3)
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 = 104.09 α = 90 b = 104.09 β = 90 c = 98.21 γ = 120
Symmetry Space Group P 64 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 2006-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR571 1.5418
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 1.75 19.51 99.6 0.059 0.054 11.2 6.7 31993 31993 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 1.75 1.84 99.6 0.381 0.287 2 5.7
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 (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 1.75 19.67 31993 30361 1623 99.43 0.17081 0.1697 0.169 0.1912 0.1903 RANDOM 16.876
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] -0.02 -0.01 -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.232 r_dihedral_angle_4_deg 19.45 r_dihedral_angle_3_deg 13.107 r_dihedral_angle_1_deg 6.281 r_scangle_it 2.994 r_scbond_it 1.854 r_angle_refined_deg 1.581 r_mcangle_it 1.158 r_mcbond_it 0.705 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.232 r_dihedral_angle_4_deg 19.45 r_dihedral_angle_3_deg 13.107 r_dihedral_angle_1_deg 6.281 r_scangle_it 2.994 r_scbond_it 1.854 r_angle_refined_deg 1.581 r_mcangle_it 1.158 r_mcbond_it 0.705 r_nbtor_refined 0.306 r_nbd_refined 0.279 r_symmetry_vdw_refined 0.194 r_metal_ion_refined 0.134 r_xyhbond_nbd_refined 0.117 r_symmetry_hbond_refined 0.116 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2001 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 40
Software Software Software Name Purpose XDS data scaling SCALA data scaling CCP4 model building REFMAC refinement XDS data reduction CCP4 phasing