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Crystal Structure of the Pectin Methylesterase from Aspergillus niger in Penultimately Deglycosylated Form (N-acetylglucosamine Stub at Asn84)
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 3.6 294 Protein (6.5 mg/mL) in 50-100 mM acetate buffer mixed 1:1 with 1.9 M ammonium sulfate, 100 mM sodium acetate, pH 3.6
Crystal Properties Matthews coefficient Solvent content 2.96 58.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.614 α = 90 b = 113.543 β = 90 c = 88.765 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 2013-11-04 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 1.75 36.16 95.6 0.084 4.5 3.94 36656 36656 19
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 1.75 1.8 89.6 0.366 3.1 3.71
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 1.75 36.16 34821 1835 95.58 0.1725 0.171 0.1803 0.2015 0.2151 RANDOM 20.727
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] 0.9 -0.23 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.974 r_dihedral_angle_4_deg 16.627 r_dihedral_angle_3_deg 10.805 r_dihedral_angle_1_deg 6.366 r_mcangle_it 1.317 r_angle_refined_deg 1.305 r_mcbond_it 0.832 r_mcbond_other 0.831 r_angle_other_deg 0.746 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.974 r_dihedral_angle_4_deg 16.627 r_dihedral_angle_3_deg 10.805 r_dihedral_angle_1_deg 6.366 r_mcangle_it 1.317 r_angle_refined_deg 1.305 r_mcbond_it 0.832 r_mcbond_other 0.831 r_angle_other_deg 0.746 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2235 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 88
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data reduction MrBUMP phasing