3CCO

Structural adaptation and conservation in quadruplex-drug recognition


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KF1PDB ENTRY 1KF1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5283300mM sodium chloride, 50mM sodium cacodylate pH 6.5, 30% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties
Matthews coefficientSolvent content
3.1460.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.35α = 90
b = 61.35β = 90
c = 43.63γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210MONOCHROMATOR2007-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.9785ESRFID14-1

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
11.9722.6998.90.05623.3103739369733
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)
1.972.041000.13410.810.8359

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 1KF12.2102520252012398.80.256640.256640.254360.30275RANDOM21.26
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]
1.390.71.39-2.09
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it3.389
r_angle_refined_deg3.306
r_scbond_it1.92
r_symmetry_vdw_refined0.397
r_nbd_refined0.394
r_nbtor_refined0.353
r_xyhbond_nbd_refined0.318
r_metal_ion_refined0.232
r_symmetry_hbond_refined0.179
r_chiral_restr0.138
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it3.389
r_angle_refined_deg3.306
r_scbond_it1.92
r_symmetry_vdw_refined0.397
r_nbd_refined0.394
r_nbtor_refined0.353
r_xyhbond_nbd_refined0.318
r_metal_ion_refined0.232
r_symmetry_hbond_refined0.179
r_chiral_restr0.138
r_symmetry_metal_ion_refined0.101
r_bond_refined_d0.019
r_gen_planes_refined0.019
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms219
Solvent Atoms28
Heterogen Atoms130

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing