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Crystal structure of the macro domain of human histone macroH2A1.1 in complex with ADP-ribose (form A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZR3 PDB entry 1ZR3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 35% PEG 1000, 0.2 M K2NO3, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.46 50.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.26 α = 90 b = 86.26 β = 90 c = 51.04 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 2006-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.973 ESRF ID29
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 1.9 19.86 99.5 0.057 23.7 10 17128 17128 -3 41
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 1.9 1.95 94.4 0.525 3.6 7.3 1220
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 1ZR3 1.9 19.86 16271 857 100 0.17769 0.17579 0.1812 0.21467 0.2263 RANDOM 32.866
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] -1.8 -0.9 -1.8 2.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.983 r_dihedral_angle_4_deg 22.509 r_dihedral_angle_3_deg 14.206 r_dihedral_angle_1_deg 9.524 r_scangle_it 2.878 r_scbond_it 2.038 r_angle_refined_deg 1.68 r_mcangle_it 1.073 r_angle_other_deg 1.002 r_mcbond_it 0.839
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.983 r_dihedral_angle_4_deg 22.509 r_dihedral_angle_3_deg 14.206 r_dihedral_angle_1_deg 9.524 r_scangle_it 2.878 r_scbond_it 2.038 r_angle_refined_deg 1.68 r_mcangle_it 1.073 r_angle_other_deg 1.002 r_mcbond_it 0.839 r_nbd_refined 0.232 r_mcbond_other 0.189 r_symmetry_vdw_refined 0.188 r_nbd_other 0.182 r_symmetry_hbond_refined 0.18 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.166 r_symmetry_vdw_other 0.163 r_chiral_restr 0.1 r_nbtor_other 0.087 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1377 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 40
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling