6UU4

E. coli sigma-S transcription initiation complex with a 3-nt RNA ("old" crystal soaked with GTP and dinucleotide GpA for 30 minutes)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5IPL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	295	PEG3350, sodium chloride, HEPES

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.143	α = 90
b = 153.432	β = 90
c = 230.958	γ = 90

Symmetry
Space Group	P 21 21 21

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-F		2017-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97918	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	4.3	49	99.6	0.999	11.74	13.4		32436

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	4.3	4.56	98.6		0.22	0.54	13.1

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5IPL	4.305	48.975	32219	1541	98.974	0.307	0.3041	0.3637	0	308.26

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]
-0.84			1.346		-0.506

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	30.074
r_lrange_other	30.057
r_dihedral_angle_2_deg	21.351
r_dihedral_angle_3_deg	15.974
r_dihedral_angle_4_deg	15.441
r_mcangle_it	14.393
r_mcangle_other	14.393
r_scangle_it	11.62
r_scangle_other	11.558
r_mcbond_it	8.22
r_mcbond_other	8.22
r_scbond_it	6.316
r_scbond_other	6.284
r_dihedral_angle_1_deg	6.123
r_angle_refined_deg	1.349
r_angle_other_deg	0.726
r_symmetry_xyhbond_nbd_refined	0.436
r_nbd_other	0.435
r_xyhbond_nbd_other	0.4
r_symmetry_nbd_refined	0.394
r_metal_ion_refined	0.354
r_symmetry_nbd_other	0.227
r_xyhbond_nbd_refined	0.225
r_nbd_refined	0.217
r_nbtor_refined	0.153
r_symmetry_xyhbond_nbd_other	0.152
r_ncsr_local_group_1	0.115
r_chiral_restr	0.056
r_gen_planes_refined	0.047
r_gen_planes_other	0.043
r_bond_refined_d	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	27482
Nucleic Acid Atoms	1441
Solvent Atoms
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing