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Crystal structure of pectin methylesterase D178A mutant in complex with hexasaccharide II
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 2.84 56.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.012 α = 90 b = 84.84 β = 93.57 c = 97.163 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 97.13 94.5 0.093 11.4 3.4 110223 16.45
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 87.4 0.379 2.7 3.1
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 97.13 83040 4382 96.35 0.20149 0.19993 0.1991 0.23124 0.2304 RANDOM 14.266
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] -0.46 0.21 0.1 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.759 r_dihedral_angle_4_deg 16.75 r_dihedral_angle_3_deg 12.013 r_dihedral_angle_1_deg 5.907 r_scangle_it 1.853 r_scbond_it 1.225 r_angle_refined_deg 1.038 r_mcangle_it 0.839 r_mcbond_it 0.481 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.759 r_dihedral_angle_4_deg 16.75 r_dihedral_angle_3_deg 12.013 r_dihedral_angle_1_deg 5.907 r_scangle_it 1.853 r_scbond_it 1.225 r_angle_refined_deg 1.038 r_mcangle_it 0.839 r_mcbond_it 0.481 r_nbtor_refined 0.306 r_nbd_refined 0.187 r_symmetry_vdw_refined 0.174 r_xyhbond_nbd_refined 0.109 r_symmetry_hbond_refined 0.097 r_chiral_restr 0.067 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 5212 Nucleic Acid Atoms Solvent Atoms 849 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing