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Crystal structure of the macro-domain of human core histone variant macroH2A1.2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HJZ homology model of macroH2A1.2 based on PDB-ID 1HJZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 25% PEG 5000MME 0.1 M Bis-Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.3 46.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.549 α = 90 b = 72.258 β = 90 c = 144.641 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 CCD MARRESEARCH 2004-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.93100 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.9 72.36 97.5 0.061 19.7 6.9 9957 9713 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.08 84.9 0.311 4.46 4.7 1342
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 homology model of macroH2A1.2 based on PDB-ID 1HJZ 2.92 72.36 -3 -3 9225 9225 487 100 0.2165 0.2165 0.21343 0.2103 0.27691 0.2724 RANDOM 58.584
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] 5.97 -0.77 -5.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.398 r_dihedral_angle_3_deg 21.945 r_dihedral_angle_4_deg 14.66 r_dihedral_angle_1_deg 6.454 r_scangle_it 2.125 r_angle_refined_deg 1.64 r_scbond_it 1.228 r_mcangle_it 0.969 r_mcbond_it 0.531 r_symmetry_vdw_refined 0.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.398 r_dihedral_angle_3_deg 21.945 r_dihedral_angle_4_deg 14.66 r_dihedral_angle_1_deg 6.454 r_scangle_it 2.125 r_angle_refined_deg 1.64 r_scbond_it 1.228 r_mcangle_it 0.969 r_mcbond_it 0.531 r_symmetry_vdw_refined 0.331 r_nbtor_refined 0.314 r_nbd_refined 0.242 r_symmetry_hbond_refined 0.167 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2848 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing