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Crystal structure of pectin methylesterase in complex with hexasaccharide V
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 2.88 57.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.094 α = 90 b = 85.33 β = 93.55 c = 97.803 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 4 monochromator 2005-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.93000 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 1.8 64.28 99.9 0.063 16.8 3.7 77539 77539 13.89
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 1.8 1.9 99.9 0.242 5.5 3.7
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 1.8 64.28 73622 3893 99.86 0.20701 0.205 0.2049 0.2439 0.2427 RANDOM 15.94
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] -0.7 0.22 0.46 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.253 r_dihedral_angle_4_deg 17.488 r_dihedral_angle_3_deg 12.887 r_dihedral_angle_1_deg 5.984 r_scangle_it 2.035 r_scbond_it 1.4 r_angle_refined_deg 1.089 r_mcangle_it 0.877 r_mcbond_it 0.504 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.253 r_dihedral_angle_4_deg 17.488 r_dihedral_angle_3_deg 12.887 r_dihedral_angle_1_deg 5.984 r_scangle_it 2.035 r_scbond_it 1.4 r_angle_refined_deg 1.089 r_mcangle_it 0.877 r_mcbond_it 0.504 r_nbtor_refined 0.308 r_nbd_refined 0.178 r_symmetry_vdw_refined 0.151 r_xyhbond_nbd_refined 0.135 r_symmetry_hbond_refined 0.127 r_chiral_restr 0.071 r_bond_refined_d 0.008 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 986 Heterogen Atoms 146
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling REFMAC phasing