3GV6

Crystal Structure of human chromobox homolog 6 (CBX6) with H3K9 peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DM1PDB entry 3DM1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529714% PEG 3350, 0.2M MgCl2, 0.1M HEPES, pH7.5 , VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
1.7329.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 28.075α = 90
b = 40.454β = 90
c = 53.376γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++VeriMax HR2009-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.765098.80.080.0810.266339633928.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.761.8289.20.4730.4731.664.1547

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3DM11.7624.855870587043798.820.213540.213540.209880.26634RANDOM26.219
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]
-1.86-0.692.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.611
r_dihedral_angle_3_deg14.161
r_dihedral_angle_4_deg13.723
r_dihedral_angle_1_deg5.914
r_scangle_it2.999
r_scbond_it1.939
r_mcangle_it1.418
r_angle_refined_deg1.39
r_mcbond_it0.879
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.611
r_dihedral_angle_3_deg14.161
r_dihedral_angle_4_deg13.723
r_dihedral_angle_1_deg5.914
r_scangle_it2.999
r_scbond_it1.939
r_mcangle_it1.418
r_angle_refined_deg1.39
r_mcbond_it0.879
r_nbtor_refined0.303
r_symmetry_vdw_refined0.223
r_nbd_refined0.187
r_xyhbond_nbd_refined0.158
r_symmetry_hbond_refined0.136
r_chiral_restr0.116
r_bond_refined_d0.014
r_gen_planes_refined0.005
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 AtomsNumber
Protein Atoms521
Nucleic Acid Atoms
Solvent Atoms49
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement