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Crystal structure of Polynucleotide Phosphorylase (PNPase) core
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.2 M ammonium nitrate, 20 % w/v PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.22 61.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159.153 α = 90 b = 159.153 β = 90 c = 157.508 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 MARMOSAIC 225 mm CCD Monochromator 2006-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
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 2.7 20 96.7 0.125 9.2 2.9 20522 19414 2 2
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) 2.7 2.76 96.7 0.432 1.8 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 THROUGHOUT 2.7 19.39 20522 19414 1053 96.81 0.27245 0.27075 0.2686 0.30572 0.3038 RANDOM 48.035
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] 0.06 0.03 0.06 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.129 r_dihedral_angle_3_deg 13.007 r_dihedral_angle_4_deg 10.4 r_scangle_it 6.87 r_dihedral_angle_1_deg 4.896 r_scbond_it 4.363 r_mcangle_it 3.731 r_mcbond_it 2.791 r_angle_refined_deg 0.746 r_symmetry_vdw_refined 0.585
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.129 r_dihedral_angle_3_deg 13.007 r_dihedral_angle_4_deg 10.4 r_scangle_it 6.87 r_dihedral_angle_1_deg 4.896 r_scbond_it 4.363 r_mcangle_it 3.731 r_mcbond_it 2.791 r_angle_refined_deg 0.746 r_symmetry_vdw_refined 0.585 r_chiral_restr 0.295 r_nbtor_refined 0.289 r_nbd_refined 0.171 r_xyhbond_nbd_refined 0.161 r_symmetry_hbond_refined 0.048 r_bond_refined_d 0.006 r_gen_planes_refined 0.001 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3630 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement