4X6A | pdb_00004x6a

Crystal structure of yeast RNA polymerase II encountering oxidative Cyclopurine DNA lesions

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	390 mM (NH4)2HPO4/NaH2PO4, PH 5.9-6.3, 50 mM dioxane, 10 mM DTT, and 10.7% - 11.6% PEG6000

Crystal Properties
Matthews coefficient	Solvent content
3.41	63.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 156.55	α = 90
b = 220.334	β = 97
c = 191.563	γ = 90

Symmetry
Space Group	C 1 2 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 315r		2013-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	0.976	ALS	5.0.3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	3.95	50	98.4	0.255	0.271	0.12	3.4	5.1		54937

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.95	4.02	97.7		0.937	0.455	0.779		4.7	2692

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	3.96	50	47410	2560	88.95	0.2513	0.2489	0.2428	0.2964	0.2905	RANDOM	147.355

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]
25.4		-13.07	-6.23		-15.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.9
r_dihedral_angle_3_deg	24.242
r_dihedral_angle_4_deg	19.886
r_mcangle_it	10.227
r_dihedral_angle_1_deg	9.224
r_mcbond_it	6.023
r_mcbond_other	6.023
r_angle_other_deg	3.67
r_angle_refined_deg	1.484
r_chiral_restr	0.084

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.9
r_dihedral_angle_3_deg	24.242
r_dihedral_angle_4_deg	19.886
r_mcangle_it	10.227
r_dihedral_angle_1_deg	9.224
r_mcbond_it	6.023
r_mcbond_other	6.023
r_angle_other_deg	3.67
r_angle_refined_deg	1.484
r_chiral_restr	0.084
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	28121
Nucleic Acid Atoms	419
Solvent Atoms
Heterogen Atoms	8

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
PHENIX	refinement
Coot	model building

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.