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Crystal structure of the Orc1 BAH domain in complex with a nucleosome core particle
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TU4 3tu4, 1M4Z, 3LZ1 experimental model PDB 1M4Z 3tu4, 1M4Z, 3LZ1 experimental model PDB 3LZ1 3tu4, 1M4Z, 3LZ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277.15 6 mM Na-Cacodylate pH 6.0, 0.4 mM Spermine-HCl, 2 mM MgCl2 and 1.75% v/v PEG 400
Crystal Properties Matthews coefficient Solvent content 2.8 60.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.254 α = 90 b = 166.428 β = 90.28 c = 168.277 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 PIXEL DECTRIS PILATUS 6M-F Cryogenically-cooled single crystal Si(220) side bounce monochromator 2017-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9791 APS 24-ID-C
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 3.3 50 97.9 0.117 0.142 0.079 5.2 3 81623 112.42
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 3.36 98.1 0.837 1.014 0.566 0.485 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3tu4, 1M4Z, 3LZ1 3.3 49.054 1.36 81181 8111 97.81 0.2167 0.213 0.2154 0.2497 0.2513 133.4376
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 22.345 f_angle_d 0.555 f_chiral_restr 0.036 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16894 Nucleic Acid Atoms 12012 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing