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Structure of the RNA pyrophosphohydrolase BdRppH in complex with GTP and magnesium
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 7 298 PEG 4000, Na acetate, pH 7, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.12 60.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.732 α = 90 b = 68.749 β = 90 c = 93.069 γ = 90
Symmetry Space Group P 21 21 21
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 RAXIS4 2008-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER 1.54
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 2.8 50 98.5 0.054 31.443 3.8 11207
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) 2.8 2.9 99.8 0.714 3.8 1119
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.8 33.61 11171 547 98.61 0.229 0.226 0.2475 0.301 0.2897 RANDOM 68.428
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] 1.87 2.28 -4.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.091 r_dihedral_angle_4_deg 23.907 r_dihedral_angle_3_deg 19.483 r_dihedral_angle_1_deg 7.828 r_scangle_it 2.063 r_angle_refined_deg 1.393 r_scbond_it 1.259 r_mcangle_it 0.711 r_mcbond_it 0.369 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.091 r_dihedral_angle_4_deg 23.907 r_dihedral_angle_3_deg 19.483 r_dihedral_angle_1_deg 7.828 r_scangle_it 2.063 r_angle_refined_deg 1.393 r_scbond_it 1.259 r_mcangle_it 0.711 r_mcbond_it 0.369 r_nbtor_refined 0.308 r_nbd_refined 0.212 r_metal_ion_refined 0.194 r_xyhbond_nbd_refined 0.15 r_symmetry_vdw_refined 0.144 r_chiral_restr 0.095 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2165 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 70
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction