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The crystal structure of an archaeal CPSF subunit, PH1404 from Pyrococcus horikoshii complexed with RNA-analog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AF5 PDB ENTRY 3AF5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.8 293 0.1M sodium acetate, 0.1M sodium chloride, 8% (v/v) PEG 6000, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.85 56.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.438 α = 90 b = 86.438 β = 90 c = 237.501 γ = 90
Symmetry Space Group P 43 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 RIGAKU JUPITER 210 2008-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0000 SPring-8 BL26B1
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 2.6 50 99.9 0.058 27.12 7.1 52847 -3 59.9
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) 2.6 2.69 99.5 0.52 2.06 5.6 5236
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 PDB ENTRY 3AF5 2.6 42.59 50924 5026 96.2 0.22 0.22 0.236 0.258 0.2727 RANDOM 66
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] 1.54 1.54 -3.08
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 3.03 c_mcangle_it 2.37 c_scbond_it 1.99 c_mcbond_it 1.38 c_angle_deg 1.3 c_improper_angle_d 0.9 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 3.03 c_mcangle_it 2.37 c_scbond_it 1.99 c_mcbond_it 1.38 c_angle_deg 1.3 c_improper_angle_d 0.9 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5099 Nucleic Acid Atoms 106 Solvent Atoms 37 Heterogen Atoms 27
Software Software Software Name Purpose BSS data collection MOLREP phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling