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The structure and function of Xenopus NO38-core, a histone binding chaperone in the nucleolus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XB9 PDB entry 1XB9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 296 PEG400, Ethylene glycol, Tris-HCl, Magnesium Chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 1.9 35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59 α = 77 b = 59 β = 88.3 c = 87.2 γ = 60.9
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 2004-01-14 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 1.7 90 79.7 0.03 0.031 9.6 4.5 109907
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) 1.7 1.76 88.2 0.182 0.155 4.2 13.7 706
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 1XB9 1.7 84.52 98408 90609 7879 89.82 0.21239 0.20834 0.2173 0.25908 0.2638 RANDOM 23.185
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] 0.3 -0.78 -0.03 0.83 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.08 r_scangle_it 4.913 r_scbond_it 3.263 r_angle_refined_deg 2.439 r_mcangle_it 2.153 r_mcbond_it 1.382 r_angle_other_deg 1.05 r_symmetry_hbond_refined 0.533 r_xyhbond_nbd_refined 0.454 r_symmetry_vdw_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.08 r_scangle_it 4.913 r_scbond_it 3.263 r_angle_refined_deg 2.439 r_mcangle_it 2.153 r_mcbond_it 1.382 r_angle_other_deg 1.05 r_symmetry_hbond_refined 0.533 r_xyhbond_nbd_refined 0.454 r_symmetry_vdw_refined 0.323 r_nbd_other 0.27 r_symmetry_vdw_other 0.263 r_nbd_refined 0.224 r_chiral_restr 0.15 r_nbtor_other 0.098 r_bond_refined_d 0.029 r_gen_planes_refined 0.013 r_gen_planes_other 0.013 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7963 Nucleic Acid Atoms Solvent Atoms 365 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling EPMR phasing