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Crystal structure of the polygalacturonase from Colletotrichum lupini and its implications for the interaction with polygalacturonase-inhibiting proteins
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CZF PDB entry 1CZF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.5 294 24% PEG3000, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.34 47.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.64 α = 90 b = 127.266 β = 90 c = 205.828 γ = 90
Symmetry Space Group P 21 21 21
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 MAR CCD 165 mm 2005-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.2 ELETTRA 5.2R
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 1.94 105.41 99.1 0.081 9.4 9.2 165995 165995 20.3
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 1.94 2.01 97.8 0.396 8.2 16003
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 1CZF 1.94 49.33 155991 8252 98.97 0.15407 0.15182 0.1678 0.19619 0.2012 RANDOM 14.117
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 0.79 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.058 r_dihedral_angle_4_deg 14.765 r_dihedral_angle_3_deg 12.284 r_dihedral_angle_1_deg 6.363 r_scangle_it 2.674 r_scbond_it 1.724 r_angle_refined_deg 1.257 r_mcangle_it 0.92 r_mcbond_it 0.558 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.058 r_dihedral_angle_4_deg 14.765 r_dihedral_angle_3_deg 12.284 r_dihedral_angle_1_deg 6.363 r_scangle_it 2.674 r_scbond_it 1.724 r_angle_refined_deg 1.257 r_mcangle_it 0.92 r_mcbond_it 0.558 r_nbtor_refined 0.303 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.193 r_symmetry_hbond_refined 0.155 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16781 Nucleic Acid Atoms Solvent Atoms 2438 Heterogen Atoms 322
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection DENZO data reduction SCALEPACK data scaling PHASER phasing