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The structure and function of Xenopus NO38-core, a histone chaperone in the nucleolus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K5J PDB Entry 1K5J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 296 PEG400, Tris-HCl, Calcium Chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.17 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 198.913 α = 90 b = 64.549 β = 113.72 c = 97.461 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 IMAGE PLATE RIGAKU RAXIS IV++ Mirrors 2002-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.9 90 94 0.038 0.031 14.5 4.9 89372
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 1.97 94 0.221 0.19 3.24 4.2 369
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1K5J 1.9 91.29 89377 81414 6598 91.1 0.20794 0.20372 0.2095 0.25504 0.2561 RANDOM 25.843
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] 0.61 -0.21 -0.88 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.779 r_scangle_it 5.362 r_scbond_it 3.673 r_angle_refined_deg 2.559 r_mcangle_it 2.402 r_mcbond_it 1.574 r_angle_other_deg 1.119 r_symmetry_hbond_refined 0.656 r_symmetry_vdw_refined 0.321 r_symmetry_vdw_other 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.779 r_scangle_it 5.362 r_scbond_it 3.673 r_angle_refined_deg 2.559 r_mcangle_it 2.402 r_mcbond_it 1.574 r_angle_other_deg 1.119 r_symmetry_hbond_refined 0.656 r_symmetry_vdw_refined 0.321 r_symmetry_vdw_other 0.316 r_nbd_other 0.273 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.2 r_chiral_restr 0.183 r_nbtor_other 0.103 r_bond_refined_d 0.033 r_gen_planes_refined 0.014 r_gen_planes_other 0.013 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8032 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling EPMR phasing