☰ Navigation Tabs
Crystal Structure of the Pectin Methylesterase from Aspergillus niger in Deglycosylated Form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XG2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.1 294 Protein (6.5 mg/mL) in 50-100 mM acetate buffer mixed 1:1 with 1.8 M ammonium sulfate, 100 mM sodium acetate, pH 4.1
Crystal Properties Matthews coefficient Solvent content 2.99 58.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.249 α = 90 b = 113.843 β = 90 c = 88.741 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 123 IMAGE PLATE RIGAKU RAXIS IV++ AXCo PX70 QUARTZ GLASS CAPILLARY OPTIC 2013-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 36.23 95.7 0.075 5.2 3.79 34221 34221
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 1.86 91.4 0.313 3.7 3.75
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 1xg2 1.8 36.23 32510 1709 95.67 0.172 0.1704 0.1799 0.2033 0.2102 RANDOM 19.485
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] 0.26 0.42 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.922 r_dihedral_angle_4_deg 18.67 r_dihedral_angle_3_deg 10.174 r_dihedral_angle_1_deg 6.51 r_angle_refined_deg 1.258 r_mcangle_it 1.181 r_angle_other_deg 0.737 r_mcbond_it 0.729 r_mcbond_other 0.727 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.922 r_dihedral_angle_4_deg 18.67 r_dihedral_angle_3_deg 10.174 r_dihedral_angle_1_deg 6.51 r_angle_refined_deg 1.258 r_mcangle_it 1.181 r_angle_other_deg 0.737 r_mcbond_it 0.729 r_mcbond_other 0.727 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2235 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 48
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data reduction MrBUMP phasing