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Crystal structure of extended-spectrum beta-lactamase BEL-1 in complex with Moxalactam
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EOE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 298 20% PEG4600, 20% MPD, 0.1M sodium citrate pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.2 44.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.53 α = 90 b = 80.91 β = 90 c = 86.64 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 PIXEL DECTRIS PILATUS 2M 2013-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.920 Diamond I04-1
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 1.85 33.58 99.7 0.08 12.6 6.2 42901 2 19.68
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 1.85 1.95 100 0.427 3.8 6.5
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 5EOE 1.85 33.58 40684 2159 99.6 0.168 0.166 0.1763 0.215 0.2205 RANDOM 27.59
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 37.066 r_dihedral_angle_4_deg 16.674 r_dihedral_angle_3_deg 12.956 r_dihedral_angle_1_deg 6.111 r_long_range_B_other 5.668 r_long_range_B_refined 5.666 r_scangle_other 3.93 r_mcangle_other 3.025 r_mcangle_it 3.024 r_scbond_it 2.616
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.066 r_dihedral_angle_4_deg 16.674 r_dihedral_angle_3_deg 12.956 r_dihedral_angle_1_deg 6.111 r_long_range_B_other 5.668 r_long_range_B_refined 5.666 r_scangle_other 3.93 r_mcangle_other 3.025 r_mcangle_it 3.024 r_scbond_it 2.616 r_scbond_other 2.615 r_mcbond_it 2.156 r_mcbond_other 2.152 r_angle_refined_deg 1.697 r_angle_other_deg 0.877 r_chiral_restr 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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 3888 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement MOLREP phasing SCALA data scaling iMOSFLM data reduction