Experiment: 1Q32

Crystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	7.8	291.15	PEG 4000, Hepes, LiSO4, DTT, 1.6.Hexanediol , pH 7.8, EVAPORATION, temperature 291.15K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.163	α = 89.39
b = 82.207	β = 85.81
c = 98.442	γ = 67.12

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 4		2001-10-24	M	MAD
2	1	x-ray	100	CCD	MARRESEARCH		2002-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12B	0.9789, 0.9796, 0.9637	NSLS	X12B
2	SYNCHROTRON	APS BEAMLINE 22-ID	1.02466	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.8	50	90.4	0.067		3.4	155815	155815		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.86	54.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.03	30	110179	110179	10979		0.21411	0.21411	0.2141	0.2235	0.2414	RANDOM

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]

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	2.937
c_mcangle_it	2.38
c_scbond_it	1.954
c_mcbond_it	1.444
c_bond_d
c_angle_deg
c_dihedral_angle_d
c_improper_angle_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13656
Nucleic Acid Atoms
Solvent Atoms	862
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing