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Crystal structure of the FHA domain of RNF8 in complex with its optimal phosphopeptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CSW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 batch crystallization 8 277 4 mM Tris pH 8, 4 mM NaCl, 0.4 mM DTT, pH 8.0, batch crystallization, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.39 48.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.632 α = 90 b = 76.865 β = 90 c = 120.744 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 ADSC QUANTUM 315 2006-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.979462 SSRL BL9-2
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 1.35 50 99.9 0.067 12.2 9 35871
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) 1.35 1.4 100 0.354 6.1 3534
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 2CSW 1.35 50 35808 1812 99.79 0.182 0.181 0.1972 0.198 0.2182 RANDOM 15.494
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] -0.65 0.85 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.279 r_dihedral_angle_4_deg 15.289 r_dihedral_angle_3_deg 12.624 r_dihedral_angle_1_deg 6.76 r_scangle_it 2.835 r_scbond_it 2.037 r_angle_refined_deg 1.539 r_mcangle_it 1.322 r_mcbond_it 1.177 r_angle_other_deg 0.908
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.279 r_dihedral_angle_4_deg 15.289 r_dihedral_angle_3_deg 12.624 r_dihedral_angle_1_deg 6.76 r_scangle_it 2.835 r_scbond_it 2.037 r_angle_refined_deg 1.539 r_mcangle_it 1.322 r_mcbond_it 1.177 r_angle_other_deg 0.908 r_symmetry_vdw_refined 0.427 r_symmetry_vdw_other 0.403 r_mcbond_other 0.226 r_nbd_refined 0.197 r_nbd_other 0.192 r_nbtor_refined 0.177 r_symmetry_hbond_refined 0.112 r_xyhbond_nbd_refined 0.1 r_chiral_restr 0.093 r_nbtor_other 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1239 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction