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First crystal structure of a psychrophile class C beta-lactamase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BLT PDB ENTRY 2BLT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 298 20% PEG 6K, 0.1M Tris, pH8.0, vapor diffusion, temperature 298K, VAPOR DIFFUSION
Crystal Properties Matthews coefficient Solvent content 2.11 41.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.6 α = 90 b = 69.7 β = 90.9 c = 53.9 γ = 90
Symmetry Space Group P 1 21 1
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 2003-04-02 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.9797 ESRF BM30A
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 2.2 20 95.4 0.038 23.94 15724 4 4
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) 2.2 2.3 99.9 0.061 16.62 7667
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION AB INITIO THROUGHOUT PDB ENTRY 2BLT 2.26 19.12 13703 13722 722 95.06 0.19224 0.18958 0.1659 0.24292 RANDOM 16.568
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] -0.01 0.01 0.01
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 2715
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.853 r_dihedral_angle_4_deg 24.201 r_dihedral_angle_3_deg 20.697 r_dihedral_angle_1_deg 6.309 r_scangle_it 2.942 r_scbond_it 1.987 r_angle_refined_deg 1.405 r_mcangle_it 1.255 r_mcbond_it 0.755 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.853 r_dihedral_angle_4_deg 24.201 r_dihedral_angle_3_deg 20.697 r_dihedral_angle_1_deg 6.309 r_scangle_it 2.942 r_scbond_it 1.987 r_angle_refined_deg 1.405 r_mcangle_it 1.255 r_mcbond_it 0.755 r_nbtor_refined 0.305 r_nbd_refined 0.228 r_symmetry_vdw_refined 0.215 r_symmetry_hbond_refined 0.202 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.097 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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 2661 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement