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Crystal Structure of Polynucleotide Phosphorylase in complex with RNase E and manganese
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 2.5 M NaCl, 9 % w/v PEG 6000, 20 mM Na- citrate, 20 mM manganese acetate , VAPOR DIFFUSION
Crystal Properties Matthews coefficient Solvent content 2.95 58.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.574 α = 90 b = 158.574 β = 90 c = 156.118 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 ADSC QUANTUM 315r 2008-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 1.07 Diamond I02
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 2.4 25.91 96.7 0.125 2.9 27941 27938 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) 2.4 2.48 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 2.4 25.91 27941 27938 1490 99.34 0.28621 0.28561 0.2809 0.29758 0.2947 RANDOM 50.586
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] -0.01 -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.144 r_dihedral_angle_3_deg 12.752 r_dihedral_angle_4_deg 12.138 r_scangle_it 5.98 r_scbond_it 3.819 r_dihedral_angle_1_deg 3.575 r_mcangle_it 2.7 r_mcbond_it 1.533 r_angle_refined_deg 0.765 r_nbtor_refined 0.284
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.144 r_dihedral_angle_3_deg 12.752 r_dihedral_angle_4_deg 12.138 r_scangle_it 5.98 r_scbond_it 3.819 r_dihedral_angle_1_deg 3.575 r_mcangle_it 2.7 r_mcbond_it 1.533 r_angle_refined_deg 0.765 r_nbtor_refined 0.284 r_nbd_refined 0.136 r_symmetry_vdw_refined 0.118 r_symmetry_hbond_refined 0.106 r_xyhbond_nbd_refined 0.096 r_chiral_restr 0.045 r_bond_refined_d 0.005 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 3694 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 2
Software Software Software Name Purpose HKL-3000 data collection REFMAC refinement