1PGZ

Crystal Structure of UP1 Complexed With d(TTAGGGTTAG(6-MI)G); A Human Telomeric Repeat Containing 6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine (6-MI)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2UP1PDB ENTRY 2UP1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.1283ammonium phosphate, glycerol, Tris, sodium chloride, MES, EDTA, beta-mercaptoethanol, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 283.0K
Crystal Properties
Matthews coefficientSolvent content
2.3747.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.622α = 90
b = 51.622β = 90
c = 171.472γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray103IMAGE PLATERIGAKU RAXIS IV++osmic mirrors2003-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

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
12.62094.90.0930.09315.25.9137471374722.3
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)
2.62.6496.10.3250.3254.45.4357

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 2UP12.619.8137471198560783.60.2370.2370.2350.269Random21
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]
3.743.74-7.48
RMS Deviations
KeyRefinement Restraint Deviation
x_torsion_deg23.7
x_angle_deg1.5
x_torsion_impr_deg1.02
x_bond_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1467
Nucleic Acid Atoms212
Solvent Atoms46
Heterogen Atoms

Software

Software
Software NamePurpose
Crystaldata collection
SCALEPACKdata scaling
CNSrefinement
CrystalCleardata reduction
CNSphasing