3QMD

Structural Basis of Selective Binding of Nonmethylated CpG Islands by the CXXC Domain of CFP1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QMBPDB 3QMB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52910.1M Hepes pH 7.5, 0.1M MgCl2, 30% PEG550MME., VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.1442.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 30.653α = 90
b = 74.688β = 90
c = 125.769γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Rosenbaum-Rock high-resolution double-crystal monochromator2010-08-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97924APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.95097.80.06712.75.511621
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.91.97880.5124.41025

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 3QMB1.932.111158554597.640.22540.22460.241RANDOM55.8028
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]
-0.11-0.240.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.722
r_dihedral_angle_4_deg22.081
r_dihedral_angle_3_deg15.918
r_dihedral_angle_1_deg5.384
r_scangle_it3.057
r_scbond_it1.899
r_angle_refined_deg1.662
r_mcangle_it1.185
r_mcbond_it0.649
r_chiral_restr0.075
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.722
r_dihedral_angle_4_deg22.081
r_dihedral_angle_3_deg15.918
r_dihedral_angle_1_deg5.384
r_scangle_it3.057
r_scbond_it1.899
r_angle_refined_deg1.662
r_mcangle_it1.185
r_mcbond_it0.649
r_chiral_restr0.075
r_bond_refined_d0.011
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms412
Nucleic Acid Atoms486
Solvent Atoms26
Heterogen Atoms2

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
EPICS-baseddata collection
datadata collection
HKL-3000data reduction
HKL-3000data scaling