6UU2 | pdb_00006uu2

E. coli sigma-S transcription initiation complex with 3-nt RNA ("Old" crystal soaked with GTP and ATP 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		295	PEG3350, sodium chloride, HEPES

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.468	α = 90
b = 153.228	β = 90
c = 229.171	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	4.4	49.7	98.6	0.999	8.01	6.6		29564

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	4.4	4.67	92.2		0.11	0.51	6.7

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 (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5IPL	4.404	49.7	29033	1380	96.78	0.3	0.2966	0.3629	0	299.369

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]
0.791			-0.637		-0.154

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	40.875
r_lrange_other	40.874
r_dihedral_angle_2_deg	21.165
r_mcangle_it	21.104
r_mcangle_other	21.104
r_scangle_it	17.221
r_scangle_other	17.213
r_dihedral_angle_3_deg	16.107
r_dihedral_angle_4_deg	14.398
r_mcbond_it	12.183
r_mcbond_other	12.183
r_scbond_it	9.479
r_scbond_other	9.476
r_dihedral_angle_1_deg	5.701
r_angle_refined_deg	1.149
r_metal_ion_refined	0.565
r_angle_other_deg	0.424
r_nbd_other	0.317
r_symmetry_nbd_refined	0.284
r_xyhbond_nbd_refined	0.233
r_nbd_refined	0.224
r_symmetry_nbd_other	0.22
r_symmetry_xyhbond_nbd_refined	0.215
r_symmetry_xyhbond_nbd_other	0.196
r_nbtor_refined	0.147
r_ncsr_local_group_1	0.104
r_gen_planes_refined	0.052
r_gen_planes_other	0.047
r_chiral_restr	0.044
r_bond_other_d	0.005
r_bond_refined_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	27482
Nucleic Acid Atoms	1431
Solvent Atoms
Heterogen Atoms	36

Software

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