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Crystal structure of pectin methylesterase D178A mutant in complex with hexasaccharide I
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 Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.86 56.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.11 α = 90 b = 85.103 β = 93.48 c = 97.281 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 Diamond (111), Ge(220), toroidal mirror 2006-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.93000 ESRF ID14-3
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 99.8 0.075 16.3 3.7 91132 13.2
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 99.6 0.151 7.6 3.6
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 86538 4567 99.73 0.1893 0.18852 0.1874 0.20389 0.203 RANDOM 14.356
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] -0.29 0.1 0.26 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.862 r_dihedral_angle_4_deg 15.531 r_dihedral_angle_3_deg 12.192 r_dihedral_angle_1_deg 5.827 r_scangle_it 2.085 r_scbond_it 1.398 r_angle_refined_deg 0.994 r_mcangle_it 0.926 r_mcbond_it 0.51 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.862 r_dihedral_angle_4_deg 15.531 r_dihedral_angle_3_deg 12.192 r_dihedral_angle_1_deg 5.827 r_scangle_it 2.085 r_scbond_it 1.398 r_angle_refined_deg 0.994 r_mcangle_it 0.926 r_mcbond_it 0.51 r_nbtor_refined 0.306 r_nbd_refined 0.182 r_symmetry_vdw_refined 0.181 r_symmetry_hbond_refined 0.105 r_xyhbond_nbd_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 789 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling REFMAC phasing