5T1I

CBX3 chromo shadow domain in complex with histone H3 peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KUPpdb entry 3kup

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529325% PEG 3350, 0.2 M sodium chloride, 0.1 M Hepes, 5% Ethylene Glycol
Crystal Properties
Matthews coefficientSolvent content
1.935.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.737α = 90
b = 34.971β = 93.32
c = 45.833γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9791829APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.645.7695.50.0520.0620.0330.99914.53.416432
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6365.80.861.1030.6780.52412.3549

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 3kup1.627.7915332108895.40.1970.1940.2392thin shells (sftools)24.65
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]
0.320.110.83-1.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.437
r_dihedral_angle_3_deg12.531
r_dihedral_angle_1_deg6.049
r_dihedral_angle_4_deg5.748
r_angle_refined_deg1.758
r_mcangle_it1.258
r_angle_other_deg0.962
r_mcbond_it0.782
r_mcbond_other0.782
r_chiral_restr0.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.437
r_dihedral_angle_3_deg12.531
r_dihedral_angle_1_deg6.049
r_dihedral_angle_4_deg5.748
r_angle_refined_deg1.758
r_mcangle_it1.258
r_angle_other_deg0.962
r_mcbond_it0.782
r_mcbond_other0.782
r_chiral_restr0.107
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_gen_planes_other0.007
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1154
Nucleic Acid Atoms
Solvent Atoms44
Heterogen Atoms12

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
PHASERphasing