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Crystal structure of the human RRP6 catalytic domain with D313N mutation in the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HBJ PDB ENTRY 2HBJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 6% PEG6000, 1.5 M sodium chloride, 0.4 mM yttrium(III) trichloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.8 56.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.9 α = 90 b = 138.9 β = 90 c = 58.4 γ = 90
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 315 2007-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C APS 24-ID-C
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 2.5 35 99.3 0.067 15 3.8 75781 75251 -1
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 2.5 2.59 99.2 0.421 3.4 7560
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2HBJ 2.5 32.74 74970 3730 99.1 0.205 0.1997 0.24 0.2376 RANDOM 61.2249
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] -8.83 -8.83 17.65
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.1 c_scangle_it 3.23 c_mcangle_it 2.49 c_scbond_it 2.05 c_mcbond_it 1.43 c_angle_deg 1.2 c_improper_angle_d 0.8 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6305 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 4
Software Software Software Name Purpose SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction MOLREP phasing