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The PUB domain functions as a p97 binding module in human peptide N-glycanase.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CCQ PDB ENTRY 2CCQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9.2 50% PEG 400, 0.1M CHES, PH 9.5, 0.2M NACL
Crystal Properties Matthews coefficient Solvent content 2.39 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.987 α = 90 b = 73.987 β = 90 c = 32.994 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 2006-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
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 1.9 24.48 99 0.09 12.8 3.1 8005 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 1.9 2 98 0.28 4 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2CCQ 1.9 25 7998 410 96.3 0.1851 0.1851 0.187 0.2231 0.1831 RANDOM
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] -2.279 -1.886 -2.279 4.559
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.247 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.247 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 766 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 11
Software Software Software Name Purpose CNS refinement MOSFLM data reduction SCALA data scaling PHASER phasing