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Crystal Structure of Pectate Lyase A (C2 form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other PelE search model comprised of residues 30-61, 70-100, 105-251, 258-280, 293-314, and 323-332. (Coordinates provided by F. Jurnak)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 Lithium sulfate, PEG 8K, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.03 39.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.549 α = 90 b = 53.802 β = 109.45 c = 71.039 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 4 2000-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C 0.9795 NSLS X8C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 31.68 92.5 0.041 29056 26888
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.88 94.4 4111
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PelE from Erwinia chrysanthemi EC16 1.8 31.68 29056 26888 2667 92.5 0.181 0.181 0.181 0.225 0.2249 random
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] -0.056 1.418 -1.676 1.732
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.5 c_scangle_it 2.615 c_scbond_it 1.892 c_mcangle_it 1.539 c_angle_deg 1.4 c_mcbond_it 1.075 c_improper_angle_d 0.71 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.5 c_scangle_it 2.615 c_scbond_it 1.892 c_mcangle_it 1.539 c_angle_deg 1.4 c_mcbond_it 1.075 c_improper_angle_d 0.71 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2718 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 5
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement