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Structure of a TEM-1 beta-lactamase insertant allosterically regulated by kanamycin and anions. Complex with sulfate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V1Z PDB ENTRY 2V1Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 RESERVOIR: MES 0.1M PH 6.5, PEG5000MME 30%(W/V), AMMONIUM SULFATE 0.2M. DROP: 0.5UL PROTEIN SOLUTION AND 0.5 UL RESERVOIR
Crystal Properties Matthews coefficient Solvent content 1.9 34.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.08 α = 90 b = 72.142 β = 90 c = 73.495 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 MARRESEARCH VERTICALLY FOCUSSING MIRROR 2007-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 EMBL/DESY, HAMBURG X12
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 1.67 18 98 0.04 18 3.6 28557
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 1.67 1.75 92.3 0.25 4.5 3.4
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2V1Z 1.67 51.5 27107 1450 98.4 0.182 0.18 0.176 0.223 RANDOM 14.7
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 34.919 r_dihedral_angle_4_deg 15.405 r_dihedral_angle_3_deg 13.508 r_dihedral_angle_1_deg 5.91 r_scangle_it 3.663 r_scbond_it 2.657 r_angle_refined_deg 1.833 r_mcangle_it 1.543 r_mcbond_it 1.373 r_angle_other_deg 1.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.919 r_dihedral_angle_4_deg 15.405 r_dihedral_angle_3_deg 13.508 r_dihedral_angle_1_deg 5.91 r_scangle_it 3.663 r_scbond_it 2.657 r_angle_refined_deg 1.833 r_mcangle_it 1.543 r_mcbond_it 1.373 r_angle_other_deg 1.086 r_symmetry_vdw_other 0.304 r_symmetry_hbond_refined 0.225 r_nbd_refined 0.214 r_nbd_other 0.201 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.153 r_symmetry_vdw_refined 0.133 r_chiral_restr 0.11 r_nbtor_other 0.09 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2087 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing