3GTL

Backtracked RNA polymerase II complex with 13mer with G<>U mismatch

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GTG	PDB entry 3GTG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM Dioxane, 10mM DTT, 9-11% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.71	66.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 170.531	α = 90
b = 222.282	β = 102.19
c = 194.813	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	MARMOSAIC 325 mm CCD		2007-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.98	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.38	50	92.3	10.5	2.5		90557

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	3.38	3.5	89.2		1.5	2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB entry 3GTG	3.38	50	85851	4515	91.06	0.27285	0.27028	0.28	0.32168	0.32	RANDOM	96.182

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]
1.57		-11.68	-4.39		-2.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.538
r_dihedral_angle_3_deg	24.019
r_dihedral_angle_4_deg	18.674
r_dihedral_angle_1_deg	7.947
r_scangle_it	1.882
r_angle_refined_deg	1.613
r_mcangle_it	1.168
r_scbond_it	1.071
r_mcbond_it	0.656
r_nbtor_refined	0.319
r_symmetry_vdw_refined	0.295
r_symmetry_hbond_refined	0.284
r_nbd_refined	0.273
r_xyhbond_nbd_refined	0.211
r_chiral_restr	0.11
r_bond_refined_d	0.013
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	28140
Nucleic Acid Atoms	1107
Solvent Atoms
Heterogen Atoms	9

Software

Software
Software Name	Purpose
MAR345	data collection
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling