5C4J

Crystal structure of a transcribing RNA Polymerase II complex reveals a complete transcription bubble

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	289	PEG 4000, SODIUM MALONATE, HEPES, DTT

Crystal Properties
Matthews coefficient	Solvent content
4.81	74.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 280.711	α = 90
b = 223.384	β = 98.14
c = 156.422	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	PIXEL	DECTRIS PILATUS 6M		2006-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	.979	APS	23-ID-D

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	4	174.08	97	0.147	10.3	5.1	80485	80485

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	4	4.104	96.1		0.61	3.7	4.3

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	4	174.08	75910	2689	97.66	0.21438	0.21249	0.23	0.271	0.28	RANDOM	231.032

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]
14.92		-22.02	-5.95		-2.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	47.628
r_dihedral_angle_3_deg	23.206
r_sphericity_bonded	20.435
r_dihedral_angle_4_deg	16.432
r_long_range_B_refined	9.687
r_mcangle_it	7.856
r_scbond_it	7.119
r_rigid_bond_restr	7.057
r_mcbond_it	6.383
r_sphericity_free	5.757
r_dihedral_angle_1_deg	2.212
r_angle_refined_deg	1.921
r_chiral_restr	0.151
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	28738
Nucleic Acid Atoms	1750
Solvent Atoms
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PHASER	phasing