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Crystal structure of pectin methylesterase in complex with hexasaccharide VI
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QJV PDB entry 1QJV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 1.6 M Ammonium sulfate, 0.1 M MES pH 6.5, 10% v/v Dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.85 56.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.091 α = 90 b = 85 β = 93.56 c = 97.325 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 MAR CCD 225 mm monochromator 2006-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 0.90000 SRS PX10.1
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 1.7 36.32 100 0.065 15 3.8 91245 91245 13.25
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 1.7 1.79 100 0.282 4.6 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 FOURIER SYNTHESIS THROUGHOUT PDB entry 1QJV 1.7 36.32 86652 4568 99.99 0.18572 0.18409 0.1835 0.21665 0.216 RANDOM 16.201
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] -0.57 0.15 0.44 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.663 r_dihedral_angle_4_deg 15.529 r_dihedral_angle_3_deg 11.748 r_dihedral_angle_1_deg 5.802 r_scangle_it 1.981 r_scbond_it 1.338 r_angle_refined_deg 1.003 r_mcangle_it 0.88 r_mcbond_it 0.49 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.663 r_dihedral_angle_4_deg 15.529 r_dihedral_angle_3_deg 11.748 r_dihedral_angle_1_deg 5.802 r_scangle_it 1.981 r_scbond_it 1.338 r_angle_refined_deg 1.003 r_mcangle_it 0.88 r_mcbond_it 0.49 r_nbtor_refined 0.306 r_nbd_refined 0.173 r_symmetry_vdw_refined 0.167 r_xyhbond_nbd_refined 0.101 r_symmetry_hbond_refined 0.098 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5218 Nucleic Acid Atoms Solvent Atoms 1038 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing