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Structural insights into the loss of catalytic competence in pectate lyase at low pH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BN8 PDB ENTRY 1BN8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 19% PEG 4K, 0.1M SODIUM ACETATE PH4, 0.2M AMMONIUM ACETATE
Crystal Properties Matthews coefficient Solvent content 2.55 51.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.78 α = 90 b = 88.12 β = 110.41 c = 55.46 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 ADSC QUANTUM 210 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 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 1.57 51.98 93 0.07 13.7 3.9 58741 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 1.57 1.66 85.5 0.36 3.5 3.8
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 PDB ENTRY 1BN8 1.57 51.98 55740 2975 92.57 0.16063 0.1589 0.1581 0.19283 0.1924 RANDOM 13.819
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] 0.14 0.07 -0.28 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.936 r_dihedral_angle_3_deg 11.516 r_dihedral_angle_4_deg 10.87 r_dihedral_angle_1_deg 6.061 r_scangle_it 3.522 r_scbond_it 2.25 r_angle_refined_deg 1.503 r_mcangle_it 1.404 r_mcbond_it 0.893 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.936 r_dihedral_angle_3_deg 11.516 r_dihedral_angle_4_deg 10.87 r_dihedral_angle_1_deg 6.061 r_scangle_it 3.522 r_scbond_it 2.25 r_angle_refined_deg 1.503 r_mcangle_it 1.404 r_mcbond_it 0.893 r_chiral_restr 0.112 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_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 3066 Nucleic Acid Atoms Solvent Atoms 590 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing