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Crystal structure of the PUB domain of mouse PNGase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 281 18-22% PEG 5000 MME and 14-18% Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties Matthews coefficient Solvent content 2.47 50.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.641 α = 90 b = 52.042 β = 115.25 c = 34.946 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 2006-03-10 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 4 2006-03-29 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418 2 SYNCHROTRON NSLS BEAMLINE X26C 1.0074 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 1.7 50 95 0.055 0.055 23.9 4.08 11390 2 2 16.8
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 1.7 1.76 56.8 0.106 0.106 6.6 1.9 682
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 SIRAS THROUGHOUT 1.7 20 2 2 10843 11387 544 94.77 0.149 0.148 0.147 0.177 0.2087 RANDOM 11.93
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] 0.94 0.03 0.11 -1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.706 r_dihedral_angle_4_deg 17.56 r_dihedral_angle_3_deg 11.856 r_dihedral_angle_1_deg 5.33 r_scangle_it 3.522 r_scbond_it 2.523 r_angle_refined_deg 1.529 r_mcangle_it 1.378 r_mcbond_it 1.277 r_angle_other_deg 0.913
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.706 r_dihedral_angle_4_deg 17.56 r_dihedral_angle_3_deg 11.856 r_dihedral_angle_1_deg 5.33 r_scangle_it 3.522 r_scbond_it 2.523 r_angle_refined_deg 1.529 r_mcangle_it 1.378 r_mcbond_it 1.277 r_angle_other_deg 0.913 r_symmetry_vdw_other 0.283 r_mcbond_other 0.282 r_nbd_refined 0.226 r_nbd_other 0.187 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.181 r_symmetry_vdw_refined 0.172 r_symmetry_hbond_refined 0.11 r_chiral_restr 0.1 r_nbtor_other 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 779 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 24
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction