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Structure of the RNA pyrophosphohydrolase BdRppH
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 2.04 39.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.491 α = 90 b = 70.491 β = 90 c = 100.481 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 CCD adsc Q210 2007-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 1.0 NSLS X6A
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 1.9 33.26 99.8 0.043 63.364 10 23316
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) 1.9 1.97 100 0.39 9 2288
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 MIR THROUGHOUT 1.9 33.26 23229 1188 99.57 0.223 0.222 0.2721 0.256 0.3002 RANDOM 40.295
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 -0.14 -0.28 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.533 r_dihedral_angle_4_deg 17.754 r_dihedral_angle_3_deg 15.794 r_dihedral_angle_1_deg 6.026 r_scangle_it 2.581 r_scbond_it 1.676 r_angle_refined_deg 1.298 r_mcangle_it 1.083 r_mcbond_it 0.677 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.533 r_dihedral_angle_4_deg 17.754 r_dihedral_angle_3_deg 15.794 r_dihedral_angle_1_deg 6.026 r_scangle_it 2.581 r_scbond_it 1.676 r_angle_refined_deg 1.298 r_mcangle_it 1.083 r_mcbond_it 0.677 r_nbtor_refined 0.302 r_symmetry_hbond_refined 0.192 r_nbd_refined 0.19 r_symmetry_vdw_refined 0.176 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2105 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection