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SHV-1 beta-lactamase complex with LP06
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VM1 PDB ENTRY 1VM1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 20-30% PEG 6000, 0.1M HEPES, 0.56Mm Cymal-6, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 1.99 38.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.554 α = 90 b = 56.484 β = 90 c = 82.067 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 315 mirrors 2007-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.91840 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 50 24.1 0.111 4.2 23654 1 11.338
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.75 1.81 99.4 0.474 2.78 4.1 2334
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 1VM1 1.75 33.92 23654 22409 1206 98.84 0.15468 0.15321 0.1541 0.18107 0.1818 RANDOM 11.271
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.323 r_dihedral_angle_4_deg 19.978 r_dihedral_angle_3_deg 12.652 r_dihedral_angle_1_deg 5.901 r_scangle_it 3.158 r_scbond_it 1.988 r_angle_refined_deg 1.564 r_mcangle_it 1.037 r_mcbond_it 0.664 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.323 r_dihedral_angle_4_deg 19.978 r_dihedral_angle_3_deg 12.652 r_dihedral_angle_1_deg 5.901 r_scangle_it 3.158 r_scbond_it 1.988 r_angle_refined_deg 1.564 r_mcangle_it 1.037 r_mcbond_it 0.664 r_nbtor_refined 0.304 r_chiral_restr 0.234 r_symmetry_vdw_refined 0.202 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.149 r_xyhbond_nbd_refined 0.128 r_bond_refined_d 0.012 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_refined 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_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2024 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 98
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling