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The Mouse PNGase-HR23 Complex Reveals a Complete Remodulation of the Protein-Protein Interface Compared to its Yeast Orthologs
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F4M PDB ENTRY 2F4M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 291 0.1 M Tris-HCl, 28-32% PEG4000, 0.2 M sodium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 8.50
Crystal Properties Matthews coefficient Solvent content 2.23 44.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.958 α = 90 b = 52.097 β = 113.5 c = 80.848 γ = 90
Symmetry Space Group C 1 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 IMAGE PLATE RIGAKU RAXIS IV 2005-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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 2.2 50 91.3 0.098 0.055 18.4 17174 17174 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 2.2 2.24 49.5 0.234 0.216 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2F4M 2.26 20 17174 14551 739 83.2 0.22 0.22 0.293 RANDOM 62.44
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] 2.75 0.86 1.29 -3.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.358 r_dihedral_angle_3_deg 18.783 r_dihedral_angle_4_deg 18.514 r_dihedral_angle_1_deg 8.003 r_scangle_it 2.041 r_angle_refined_deg 1.559 r_scbond_it 1.408 r_mcangle_it 0.891 r_angle_other_deg 0.879 r_mcbond_it 0.711
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.358 r_dihedral_angle_3_deg 18.783 r_dihedral_angle_4_deg 18.514 r_dihedral_angle_1_deg 8.003 r_scangle_it 2.041 r_angle_refined_deg 1.559 r_scbond_it 1.408 r_mcangle_it 0.891 r_angle_other_deg 0.879 r_mcbond_it 0.711 r_symmetry_vdw_refined 0.286 r_nbd_refined 0.235 r_xyhbond_nbd_refined 0.209 r_nbd_other 0.197 r_symmetry_vdw_other 0.183 r_nbtor_refined 0.182 r_mcbond_other 0.144 r_symmetry_hbond_refined 0.111 r_nbtor_other 0.089 r_chiral_restr 0.084 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2945 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 3
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing