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Structure of SHV-1 beta-lactamase in complex with the 7-alkylidenecephalosporin DCM-1-10 at 1.14 Ang resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SHV pdb entry 1SHV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 21-30% PEG 6000, 0.1M HEPES buffer, 0.56mM Cymal-6, pH 6.8-7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.84 32.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.308 α = 90 b = 55.222 β = 90 c = 84.285 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 315r 2010-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.97946 SSRL BL7-1
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 1.14 24.41 95.18 0.038 0.038 13.8 3.6 79862 76013 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.14 1.18 77.2 0.351 3.2
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 1SHV 1.14 24.41 79862 76013 3993 95.18 0.13223 0.13054 0.1299 0.16362 0.1633 RANDOM 15.605
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] -0.07 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.917 r_sphericity_free 18.702 r_dihedral_angle_4_deg 18.638 r_dihedral_angle_3_deg 11.941 r_sphericity_bonded 9.086 r_scangle_it 8.268 r_scbond_it 6.057 r_dihedral_angle_1_deg 5.999 r_mcangle_it 3.861 r_rigid_bond_restr 3.638
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.917 r_sphericity_free 18.702 r_dihedral_angle_4_deg 18.638 r_dihedral_angle_3_deg 11.941 r_sphericity_bonded 9.086 r_scangle_it 8.268 r_scbond_it 6.057 r_dihedral_angle_1_deg 5.999 r_mcangle_it 3.861 r_rigid_bond_restr 3.638 r_mcbond_it 2.945 r_angle_refined_deg 1.459 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2024 Nucleic Acid Atoms Solvent Atoms 338 Heterogen Atoms 77
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling