☰ Navigation Tabs
Crystal structure of human chromobox homolog 1 (CBX1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DM1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 30% PEG 400, 0.2M CaCl2 0.1M Na Hepes 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.98 37.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.057 α = 90 b = 39.068 β = 137.03 c = 37.832 γ = 90
Symmetry Space Group C 1 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 CCD MARMOSAIC 300 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.97625 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 40 4815 4818
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 3DM1 1.8 27.18 4660 219 96.74 0.224 0.222 0.224 0.274 0.2752 RANDOM 11.545
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] 0.97 1.78 -1.2 2.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.944 r_dihedral_angle_4_deg 13.996 r_dihedral_angle_3_deg 11.622 r_dihedral_angle_1_deg 6.397 r_scangle_it 3.111 r_scbond_it 2.314 r_angle_refined_deg 1.623 r_mcangle_it 1.346 r_mcbond_it 0.962 r_symmetry_hbond_refined 0.393
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.944 r_dihedral_angle_4_deg 13.996 r_dihedral_angle_3_deg 11.622 r_dihedral_angle_1_deg 6.397 r_scangle_it 3.111 r_scbond_it 2.314 r_angle_refined_deg 1.623 r_mcangle_it 1.346 r_mcbond_it 0.962 r_symmetry_hbond_refined 0.393 r_symmetry_vdw_refined 0.36 r_nbtor_refined 0.311 r_xyhbond_nbd_refined 0.23 r_nbd_refined 0.223 r_chiral_restr 0.106 r_bond_refined_d 0.019 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 393 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction