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Crystal structure of extended-spectrum beta-lactamase BEL-1 (orthorhombic form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IYS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 298 15% PEG 4000, 15% 2-propanol, 0.1M sodium citrate, pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.66 53.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.27 α = 90 b = 120.92 β = 90 c = 53.41 γ = 90
Symmetry Space Group P 21 21 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 CCD ADSC QUANTUM 210r 2007-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 1.6 29.25 99.9 0.076 25 13.6 86406 2 14.112
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 1.6 1.69 99.9 0.397 6.9 13.6
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 1IYS 1.6 29.25 82015 4328 99.88 0.14291 0.1416 0.16707 0.1724 RANDOM 14.585
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 33.674 r_dihedral_angle_4_deg 20.582 r_dihedral_angle_3_deg 11.802 r_dihedral_angle_1_deg 5.733 r_long_range_B_refined 5.604 r_long_range_B_other 5.603 r_scangle_other 2.141 r_angle_refined_deg 1.677 r_scbond_it 1.448 r_scbond_other 1.448
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.674 r_dihedral_angle_4_deg 20.582 r_dihedral_angle_3_deg 11.802 r_dihedral_angle_1_deg 5.733 r_long_range_B_refined 5.604 r_long_range_B_other 5.603 r_scangle_other 2.141 r_angle_refined_deg 1.677 r_scbond_it 1.448 r_scbond_other 1.448 r_mcangle_other 1.376 r_mcangle_it 1.372 r_mcbond_it 0.888 r_mcbond_other 0.874 r_angle_other_deg 0.863 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4009 Nucleic Acid Atoms Solvent Atoms 800 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement MOLREP phasing MOSFLM data reduction SCALA data scaling