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Crystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1.5 microliter of the protein solution mixed with with 1.5 microliter of the reservoir solution containing 40% PEG 550 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.36 63.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.671 α = 90 b = 83.671 β = 90 c = 110.288 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2008-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ DW 1.28268
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.4 40 99.9 0.088 24.63 10.52 17856
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 100 0.836 4.38 8.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.4 39.1 17856 908 99.83 0.2219 0.21951 0.2148 0.26725 0.262 RANDOM 42.532
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] 0.12 0.06 0.12 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.057 r_dihedral_angle_3_deg 14.956 r_dihedral_angle_4_deg 14.559 r_dihedral_angle_1_deg 6.515 r_scangle_it 4.211 r_scbond_it 2.784 r_mcangle_it 2.072 r_angle_refined_deg 1.826 r_mcbond_it 1.215 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.057 r_dihedral_angle_3_deg 14.956 r_dihedral_angle_4_deg 14.559 r_dihedral_angle_1_deg 6.515 r_scangle_it 4.211 r_scbond_it 2.784 r_mcangle_it 2.072 r_angle_refined_deg 1.826 r_mcbond_it 1.215 r_nbtor_refined 0.312 r_symmetry_hbond_refined 0.286 r_xyhbond_nbd_refined 0.278 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.18 r_chiral_restr 0.118 r_bond_refined_d 0.021 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2010 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling SHELXD phasing