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Structural insights into nucleosome reorganization by NAP1-RELATED PROTEIN 1 (NRP1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DAY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 1 M NaCl, 0.1 M sodium cacodylate, 30% (v/v) PEG 600, 10% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 3.09 60.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.71 α = 90 b = 128.396 β = 90 c = 140.275 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS EIGER X 16M 2017-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9793 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3 30 96.9 0.093 0.099 0.033 7.4 7.6 24251
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.11 85 0.393 0.452 0.215 0.167 3.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5DAY 3 29.62 20062 1042 84.93 0.2248 0.2229 0.2617 0.2346 RANDOM 74.159
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] -1.42 2.82 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.475 r_dihedral_angle_4_deg 22.414 r_dihedral_angle_3_deg 21.388 r_dihedral_angle_1_deg 7.963 r_angle_refined_deg 1.54 r_angle_other_deg 1.258 r_chiral_restr 0.07 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.475 r_dihedral_angle_4_deg 22.414 r_dihedral_angle_3_deg 21.388 r_dihedral_angle_1_deg 7.963 r_angle_refined_deg 1.54 r_angle_other_deg 1.258 r_chiral_restr 0.07 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5454 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PDB_EXTRACT data extraction REFMAC phasing