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Crystal Structure of the S. pombe Peptidase Homology Domain of FACT complex subunit Spt16 (form B)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CB5 PDB ENTRY 3CB5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 20% PEG 300, 0.1M Mes, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.73 54.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.98 α = 90 b = 193.67 β = 90 c = 89.48 γ = 90
Symmetry Space Group C 2 2 21
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 MARMOSAIC 300 mm CCD 2007-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9699 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.84 19.85 99.6 0.058 20.49 7 47917 47711 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.84 1.95 98.4 0.373 4.1 4.5 7564
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3CB5 1.84 19.85 -3 45322 45322 2386 100 0.193 0.19371 0.19209 0.197 0.22472 0.2297 RANDOM 22.018
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] 1.99 -0.88 -1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.779 r_dihedral_angle_4_deg 22.038 r_dihedral_angle_3_deg 13.575 r_dihedral_angle_1_deg 5.49 r_scangle_it 3.216 r_scbond_it 2.018 r_angle_other_deg 1.302 r_angle_refined_deg 1.258 r_mcangle_it 1.199 r_mcbond_it 0.651
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.779 r_dihedral_angle_4_deg 22.038 r_dihedral_angle_3_deg 13.575 r_dihedral_angle_1_deg 5.49 r_scangle_it 3.216 r_scbond_it 2.018 r_angle_other_deg 1.302 r_angle_refined_deg 1.258 r_mcangle_it 1.199 r_mcbond_it 0.651 r_mcbond_other 0.183 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3475 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing