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Structural insights into substrate specificity and the anti beta-elimination mechanism of pectate lyase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O0V PDB entry 2O0V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 25% PEG 4000, 0.2M ammonium acetate, 0.1M sodium acetate, 50% PEG, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 44.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.626 α = 90 b = 69.066 β = 113.85 c = 59.656 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 MARMOSAIC 225 mm CCD mirrors 2007-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 0.970 SRS PX10.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 69.01 97.2 0.057 0.067 23.8 3.7 28827 8.608
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 2 96.1 0.067 0.067 18.3 3.7 4138
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 2O0V 1.9 29.18 27344 1459 96.88 0.135 0.132 0.1257 0.196 0.188 RANDOM 8.969
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.383 r_dihedral_angle_3_deg 12.384 r_dihedral_angle_4_deg 11.667 r_dihedral_angle_1_deg 6.498 r_scangle_it 3.646 r_scbond_it 2.676 r_angle_refined_deg 1.648 r_mcangle_it 1.444 r_mcbond_it 0.787 r_chiral_restr 0.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.383 r_dihedral_angle_3_deg 12.384 r_dihedral_angle_4_deg 11.667 r_dihedral_angle_1_deg 6.498 r_scangle_it 3.646 r_scbond_it 2.676 r_angle_refined_deg 1.648 r_mcangle_it 1.444 r_mcbond_it 0.787 r_chiral_restr 0.135 r_bond_refined_d 0.018 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3055 Nucleic Acid Atoms Solvent Atoms 723 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling