☰ Navigation Tabs
Crystal structure of the Bacillus subtilis pyrophosphohydrolase BsRppH bound to a non-hydrolysable triphosphorylated dinucleotide RNA (pcp-pGpG) - second guanosine residue in guanosine binding pocket
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other STRUCTURE OF BSRPPH E68A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 293 100 mM Hepes pH 7.5, 25% PEG 1000, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.06 40.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.158 α = 90 b = 138.025 β = 90 c = 35.684 γ = 90
Symmetry Space Group P 21 21 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 CCD ADSC QUANTUM 315r 2012-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.2 69.01 98.6 0.057 18.1 3.8 16071 -3
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 2.32 95.1 0.64 2.3 3.7
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 STRUCTURE OF BSRPPH E68A 2.2 28.34 16024 825 98.2 0.221 0.22 0.2351 0.241 0.2642 RANDOM 51.9
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] -3.3936 3.9511 -0.5576
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.6 t_omega_torsion 1.91 t_angle_deg 0.94 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.6 t_omega_torsion 1.91 t_angle_deg 0.94 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2558 Nucleic Acid Atoms 37 Solvent Atoms 70 Heterogen Atoms 18
Software Software Software Name Purpose SCALA data scaling PHASER phasing BUSTER-TNT refinement PDB_EXTRACT data extraction XDS data reduction BUSTER refinement