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Crystal structure of mouse Peptide N-Glycanase C-terminal domain in complex with mannopentaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G9F PDB entry 2G9F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 19 % PEG 4000, 11.5 % Isopropanol, 0.1 M Tris-HCl, pH 7.5, 0.2 M Calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.04 39.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.706 α = 90 b = 41.646 β = 94.89 c = 94.9 γ = 90
Symmetry Space Group P 1 21 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 315 2006-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 0.97950 NSLS X25
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 1.75 50 99.9 0.087 0.087 20 5.5 35889 35889 16.6
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 1.75 1.81 100 0.441 0.441 3.3 5.5 3565
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2G9F 1.75 20 2 35889 35851 1856 99.67 0.174 0.172 0.1797 0.208 0.2156 RANDOM 13.838
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] 1.05 0.44 -0.59 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.553 r_dihedral_angle_4_deg 14.186 r_dihedral_angle_3_deg 12.526 r_dihedral_angle_1_deg 6.591 r_scangle_it 3.24 r_scbond_it 2.309 r_angle_other_deg 1.668 r_angle_refined_deg 1.543 r_mcangle_it 1.294 r_mcbond_it 1.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.553 r_dihedral_angle_4_deg 14.186 r_dihedral_angle_3_deg 12.526 r_dihedral_angle_1_deg 6.591 r_scangle_it 3.24 r_scbond_it 2.309 r_angle_other_deg 1.668 r_angle_refined_deg 1.543 r_mcangle_it 1.294 r_mcbond_it 1.127 r_symmetry_vdw_refined 0.401 r_symmetry_vdw_other 0.346 r_mcbond_other 0.251 r_nbd_other 0.234 r_symmetry_hbond_refined 0.221 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.215 r_nbtor_refined 0.181 r_chiral_restr 0.125 r_nbtor_other 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2915 Nucleic Acid Atoms Solvent Atoms 321 Heterogen Atoms 132
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction MOLREP phasing