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Complex of yeast PNGase with GlcNAc2-IAc.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X3Z PDB ENTRY 1X3Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 8.5 291 0.1 M Tris-HCl, pH 8.5 and 2.0 M sodium chloride, EVAPORATION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 6.68 81.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.53 α = 90 b = 131.53 β = 90 c = 127.751 γ = 120
Symmetry Space Group P 31 2 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 2006-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 1 NSLS X26C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 3.4 37.969 99.9 0.126 0.126 5.496 8 17986 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.4 3.58 100 0.457 0.457 4.4 8.1 2581
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 THROUGHOUT PDB ENTRY 1X3Z 3.4 37.96 17961 1084 99.99 0.199 0.197 0.1955 0.235 0.234 RANDOM 63.61
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] 6.04 3.02 6.04 -9.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.589 r_dihedral_angle_3_deg 22.011 r_dihedral_angle_4_deg 19.061 r_dihedral_angle_1_deg 8.674 r_scangle_it 2.157 r_angle_refined_deg 1.599 r_scbond_it 1.236 r_mcangle_it 1.183 r_angle_other_deg 0.952 r_mcbond_it 0.619
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.589 r_dihedral_angle_3_deg 22.011 r_dihedral_angle_4_deg 19.061 r_dihedral_angle_1_deg 8.674 r_scangle_it 2.157 r_angle_refined_deg 1.599 r_scbond_it 1.236 r_mcangle_it 1.183 r_angle_other_deg 0.952 r_mcbond_it 0.619 r_chiral_restr 0.088 r_mcbond_other 0.067 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3184 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 29
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection DENZO data reduction SCALEPACK data scaling