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Structure of the RNA pyrophosphohydrolase BdRppH in complex with Holmium
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 4 298 PEG 4000, Na acetate, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.02 38.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.212 α = 90 b = 70.212 β = 90 c = 99.915 γ = 120
Symmetry Space Group P 32 2 1
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 2006-05-26 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 50 99.9 0.039 43.438 5.4 19802
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 2.07 100 0.775 5.2 1934
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 2 30.4 19758 999 99.92 0.218 0.216 0.256 0.2745 RANDOM 45.414
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] -0.4 -0.2 -0.4 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.965 r_dihedral_angle_3_deg 16.128 r_dihedral_angle_4_deg 14.236 r_dihedral_angle_1_deg 6.009 r_scangle_it 2.407 r_scbond_it 1.654 r_angle_refined_deg 1.361 r_mcangle_it 0.966 r_mcbond_it 0.621 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.965 r_dihedral_angle_3_deg 16.128 r_dihedral_angle_4_deg 14.236 r_dihedral_angle_1_deg 6.009 r_scangle_it 2.407 r_scbond_it 1.654 r_angle_refined_deg 1.361 r_mcangle_it 0.966 r_mcbond_it 0.621 r_nbtor_refined 0.302 r_symmetry_hbond_refined 0.257 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.162 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.097 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_metal_ion_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2127 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 11
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction AMoRE phasing