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Crystal structure of His-tagged mouse PNGase C-terminal domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G2F pdb entry 2G2F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 1.6 M Li2SO4 and 100 mM Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.93 36.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.732 α = 90 b = 40.747 β = 95.34 c = 66.506 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 CCD ADSC QUANTUM 4 2004-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 0.9996 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 2 50 99.9 0.108 0.108 17.8 4.6 13124 13124 21.5
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 2.07 99.4 0.485 0.485 3.9 4.5 1311
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 2G2F 2 20 13124 12453 646 99.74 0.15304 0.15304 0.15028 0.20711 0.2504 RANDOM 29.721
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] 0.22 0.07 -0.3 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.439 r_dihedral_angle_3_deg 15.344 r_dihedral_angle_4_deg 12.393 r_dihedral_angle_1_deg 7.117 r_scangle_it 6.502 r_scbond_it 4.917 r_mcangle_it 3.315 r_mcbond_it 2.811 r_angle_refined_deg 1.495 r_angle_other_deg 0.839
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.439 r_dihedral_angle_3_deg 15.344 r_dihedral_angle_4_deg 12.393 r_dihedral_angle_1_deg 7.117 r_scangle_it 6.502 r_scbond_it 4.917 r_mcangle_it 3.315 r_mcbond_it 2.811 r_angle_refined_deg 1.495 r_angle_other_deg 0.839 r_mcbond_other 0.761 r_symmetry_vdw_other 0.28 r_symmetry_hbond_refined 0.2 r_xyhbond_nbd_refined 0.198 r_nbd_other 0.189 r_nbtor_refined 0.179 r_nbd_refined 0.177 r_chiral_restr 0.096 r_nbtor_other 0.082 r_symmetry_vdw_refined 0.022 r_bond_refined_d 0.014 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 1533 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing