1PGZ | pdb_00001pgz

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)
Type	Source	Accession Code	Details
experimental model	PDB	2UP1	PDB ENTRY 2UP1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.1	283	ammonium phosphate, glycerol, Tris, sodium chloride, MES, EDTA, beta-mercaptoethanol, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 283.0K

Crystal Properties
Matthews coefficient	Solvent content
2.37	47.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.622	α = 90
b = 51.622	β = 90
c = 171.472	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	103	IMAGE PLATE	RIGAKU RAXIS IV++	osmic mirrors	2003-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.6	20	94.9	0.093	0.093	15.2	5.9	13747	13747			22.3

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)	Redundancy	Number Unique Reflections (All)
	2.6	2.64	96.1		0.325	0.325	4.4	5.4	357

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2UP1	2.6	19.8	13747	11985	607	83.6	0.237	0.237	0.235	0.22	0.269	0.26	Random	21

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]
3.74			3.74		-7.48

RMS Deviations
Key	Refinement Restraint Deviation
x_torsion_deg	23.7
x_angle_deg	1.5
x_torsion_impr_deg	1.02
x_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1467
Nucleic Acid Atoms	212
Solvent Atoms	46
Heterogen Atoms

Software

Software
Software Name	Purpose
Crystal	data collection
SCALEPACK	data scaling
CNS	refinement
CrystalClear	data reduction
CNS	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.