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Crystal structure of the macro-domain of human core histone variant macroH2A1.1 (form B)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZQ0 PDP ID 1ZQ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Microbridge 6.5 298 22% PEG 1000 0.1 M Mes pH6.5, Microbridge, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.8 31.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.9 α = 90 b = 89.2 β = 90 c = 92.73 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 ADSC QUANTUM 4 2005-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.953720 ESRF ID14-4
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 1.66 64.28 0.054 21.06 7.2 79853 78100 -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 1.66 1.76 86.4 0.484 2.41 3
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 PDP ID 1ZQ0 1.66 64.28 74190 74190 3905 100 0.19034 0.18819 0.1949 0.23166 0.2359 RANDOM 31.026
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] -0.1 0.4 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.665 r_dihedral_angle_4_deg 24.262 r_dihedral_angle_3_deg 15.065 r_dihedral_angle_1_deg 6.216 r_scangle_it 4.275 r_scbond_it 2.799 r_angle_refined_deg 1.792 r_mcangle_it 1.586 r_mcbond_it 0.999 r_angle_other_deg 0.833
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.665 r_dihedral_angle_4_deg 24.262 r_dihedral_angle_3_deg 15.065 r_dihedral_angle_1_deg 6.216 r_scangle_it 4.275 r_scbond_it 2.799 r_angle_refined_deg 1.792 r_mcangle_it 1.586 r_mcbond_it 0.999 r_angle_other_deg 0.833 r_symmetry_vdw_refined 0.382 r_mcbond_other 0.288 r_nbd_refined 0.235 r_symmetry_vdw_other 0.228 r_nbtor_refined 0.202 r_symmetry_hbond_refined 0.194 r_nbd_other 0.187 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.15 r_nbtor_other 0.095 r_bond_refined_d 0.021 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5567 Nucleic Acid Atoms Solvent Atoms 447 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing