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Crystal structure of human PNPase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GCM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 10%(v/v) 2-Propanol, 0.1M Sodium citrate tribasic dihydrate, 26%(v/v) Polyethylene glycol 400 , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.72 54.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 289.753 α = 90 b = 289.753 β = 90 c = 92.785 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 CCD RAYONIX MX300HE 2011-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 1.0 NSRRC BL13C1
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 2.13 30 100 0.046 30.8 3.2 162293 162293 34.39
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 2.13 2.21 100 0.311 4.7 3.1 16272
Refinement Statistics Diffraction ID Structure Solution 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 (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 3GCM 2.13 28.5 1.97 162282 162282 8129 99.96 0.1821 0.1799 0.1774 0.223 0.2201 RANDOM 42.4901
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] -3.1554 -3.1554 7.3758
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.781 f_angle_d 1.071 f_chiral_restr 0.079 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18929 Nucleic Acid Atoms Solvent Atoms 1172 Heterogen Atoms 104
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling