☰ Navigation Tabs
Crystal structure of the zinc-beta-lactamase L1 from stenotrophomonas maltophilia (inhibitor 1)
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 2.78 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.88 α = 90 b = 105.88 β = 90 c = 197.86 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 MULTILAYERS OSMICS 2006-03-08 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 1.8 19.83 99.81 0.062 0.062 9.9 6.8 58042
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 99.8 0.355 0.368 2.2 6.2
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 19.83 58042 3099 99.81 0.1977 0.19555 0.1955 0.23926 0.2386 RANDOM 20.131
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] 0.03 0.02 0.03 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.362 r_dihedral_angle_4_deg 18.431 r_dihedral_angle_3_deg 13.585 r_dihedral_angle_1_deg 6.631 r_sphericity_free 6.292 r_scangle_it 3.62 r_scbond_it 2.366 r_angle_refined_deg 1.689 r_mcangle_it 1.416 r_mcbond_it 0.957
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.362 r_dihedral_angle_4_deg 18.431 r_dihedral_angle_3_deg 13.585 r_dihedral_angle_1_deg 6.631 r_sphericity_free 6.292 r_scangle_it 3.62 r_scbond_it 2.366 r_angle_refined_deg 1.689 r_mcangle_it 1.416 r_mcbond_it 0.957 r_nbtor_refined 0.296 r_nbd_refined 0.283 r_symmetry_vdw_refined 0.198 r_symmetry_hbond_refined 0.165 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.099 r_metal_ion_refined 0.079 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 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 487 Heterogen Atoms 90
Software Software Software Name Purpose XDS data scaling SCALA data scaling CCP4 model building REFMAC refinement XDS data reduction CCP4 data scaling CCP4 phasing