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Crystal Structure of phi29 pRNA domain II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MGM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 0.12 mM spermine, 5 mM cobalt hexamine, 10%(+/-)-2-methyl-2,4-pentanediol (MPD), 62 mM potassium chloride, 30 mM barium chloride, 40 mM pH 6 Na cacodylate
Crystal Properties Matthews coefficient Solvent content 5.39 77.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.178 α = 90 b = 120.178 β = 90 c = 187.494 γ = 90
Symmetry Space Group I 4 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2016-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 1.606 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 3.32 101.18 99.9 0.041 13.9 8.5 10506
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.32 3.59 0.067 0.029
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 4MGM 3.32 101.18 9296 1034 98.22 0.22702 0.22291 0.2354 0.26515 0.274 RANDOM 152.093
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] -0.28 -0.28 0.55
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 22.941 r_long_range_B_other 22.938 r_scangle_other 21.038 r_scbond_it 14.001 r_scbond_other 14 r_angle_other_deg 1.561 r_angle_refined_deg 1.209 r_chiral_restr 0.085 r_gen_planes_refined 0.008 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 22.941 r_long_range_B_other 22.938 r_scangle_other 21.038 r_scbond_it 14.001 r_scbond_other 14 r_angle_other_deg 1.561 r_angle_refined_deg 1.209 r_chiral_restr 0.085 r_gen_planes_refined 0.008 r_bond_refined_d 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.003 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2077 Solvent Atoms Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling