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Catalytic function and substrate recognition of the pectate lyase from Thermotoga maritima
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BSP PDB ENTRY 2BSP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.2 pH 4.2
Crystal Properties Matthews coefficient Solvent content 2.46 50.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.602 α = 90 b = 80.602 β = 90 c = 148.819 γ = 120
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 SX-165 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 1.95 14 100 0.1 18.6 5.6 26478 2
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 1.95 14 100 0.44 3.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BSP 1.94 63.25 25137 1339 99.62 0.18168 0.17877 0.23699 0.257 RANDOM 33.708
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] 0.9 0.45 0.9 -1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.455 r_dihedral_angle_4_deg 16.404 r_dihedral_angle_3_deg 14.75 r_dihedral_angle_1_deg 6.893 r_scangle_it 3.619 r_scbond_it 2.458 r_angle_refined_deg 1.699 r_mcangle_it 1.67 r_mcbond_it 1.019 r_nbtor_refined 0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.455 r_dihedral_angle_4_deg 16.404 r_dihedral_angle_3_deg 14.75 r_dihedral_angle_1_deg 6.893 r_scangle_it 3.619 r_scbond_it 2.458 r_angle_refined_deg 1.699 r_mcangle_it 1.67 r_mcbond_it 1.019 r_nbtor_refined 0.326 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.202 r_xyhbond_nbd_refined 0.158 r_symmetry_hbond_refined 0.148 r_chiral_restr 0.132 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 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_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 2568 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement DENZO data reduction EPMR phasing