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Structure of S. pombe Dbp5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J0S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 8 288 100mM Tris, 200mM Ca(Ac)2, 8.5-10% PEG4000, pH 8.0, EVAPORATION, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.92 57.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.736 α = 90 b = 144.044 β = 89.96 c = 79.137 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 2008-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9725 ESRF ID29
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 2.8 44.81 98.5 0.064 12.6 3.6 29528 72
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 2.8 2.9 0.343 2.1 3.7 2902
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 2j0s 2.8 20 28004 1489 98.59 0.29156 0.28964 0.2907 0.32703 0.3257 RANDOM 16.869
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] 7.82 -0.5 1.15 -8.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.4 r_dihedral_angle_3_deg 22.919 r_dihedral_angle_4_deg 21.965 r_dihedral_angle_1_deg 6.263 r_scangle_it 2.033 r_angle_refined_deg 1.359 r_scbond_it 1.266 r_mcangle_it 0.954 r_mcbond_it 0.515 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.4 r_dihedral_angle_3_deg 22.919 r_dihedral_angle_4_deg 21.965 r_dihedral_angle_1_deg 6.263 r_scangle_it 2.033 r_angle_refined_deg 1.359 r_scbond_it 1.266 r_mcangle_it 0.954 r_mcbond_it 0.515 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4771 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling