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Crystal structure of the macro-domain of human core histone variant macroH2A1.1 (form A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZR5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 10% PEG8000, 0.1M NACL, 0.1M TRIS/ HCL PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2 39.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.77 α = 90 b = 98.27 β = 90 c = 42.05 γ = 90
Symmetry Space Group P 21 21 2
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 2004-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.931 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 2.54 90.91 99 0.079 16.12 6.7 12857 12857 -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) 2.54 2.7 96.3 0.299 4.48 4.6 1965
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1ZR5 2.54 90.91 -3 12335 12212 643 99 0.21 0.21 0.207 0.27 RANDOM 56.289
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] -0.85 0.22 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.136 r_dihedral_angle_3_deg 20.406 r_dihedral_angle_4_deg 18.789 r_dihedral_angle_1_deg 7.074 r_scangle_it 1.865 r_angle_refined_deg 1.519 r_scbond_it 1.195 r_mcangle_it 0.835 r_angle_other_deg 0.814 r_mcbond_it 0.623
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.136 r_dihedral_angle_3_deg 20.406 r_dihedral_angle_4_deg 18.789 r_dihedral_angle_1_deg 7.074 r_scangle_it 1.865 r_angle_refined_deg 1.519 r_scbond_it 1.195 r_mcangle_it 0.835 r_angle_other_deg 0.814 r_mcbond_it 0.623 r_symmetry_hbond_refined 0.349 r_nbd_refined 0.233 r_symmetry_vdw_other 0.212 r_xyhbond_nbd_refined 0.196 r_nbtor_refined 0.187 r_nbd_other 0.18 r_symmetry_vdw_refined 0.147 r_mcbond_other 0.101 r_nbtor_other 0.091 r_chiral_restr 0.085 r_xyhbond_nbd_other 0.07 r_bond_refined_d 0.014 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2810 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms
Software Software Software Name Purpose XDS data scaling XDS data reduction PHASER phasing REFMAC refinement