☰ Navigation Tabs
Crystal structure of the macro domain of human histone macroH2A1.1 in complex with ADP-ribose (form B)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IID PDB entry 3IID
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 294 0.8 M (NH4)2SO4, 0.2 M Sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.1 60.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.61 α = 90 b = 129.61 β = 90 c = 128.29 γ = 120
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 315r 2006-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.976 ESRF ID23-1
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 2.1 64.82 99.7 0.074 14 5.1 46730 46730 -3 37
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 2.1 2.16 96.2 0.482 3.2 4.1 3651
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3IID 2.1 64.82 44389 2337 100 0.1813 0.18005 0.1848 0.20459 0.2053 RANDOM 29.855
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] 0.06 0.03 0.06 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.768 r_dihedral_angle_4_deg 20.638 r_dihedral_angle_3_deg 17.558 r_dihedral_angle_1_deg 8.018 r_scangle_it 2.883 r_scbond_it 1.952 r_angle_refined_deg 1.662 r_mcangle_it 1.068 r_angle_other_deg 1.021 r_mcbond_it 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.768 r_dihedral_angle_4_deg 20.638 r_dihedral_angle_3_deg 17.558 r_dihedral_angle_1_deg 8.018 r_scangle_it 2.883 r_scbond_it 1.952 r_angle_refined_deg 1.662 r_mcangle_it 1.068 r_angle_other_deg 1.021 r_mcbond_it 0.84 r_nbd_refined 0.212 r_symmetry_vdw_other 0.204 r_symmetry_hbond_refined 0.192 r_nbd_other 0.185 r_nbtor_refined 0.176 r_mcbond_other 0.162 r_xyhbond_nbd_refined 0.157 r_symmetry_vdw_refined 0.133 r_chiral_restr 0.096 r_nbtor_other 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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 4101 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 108
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling