6UU9 | pdb_00006uu9

E. coli mutant sigma-S transcription initiation complex with an 8-nt RNA ("Fresh" mutant crystal soaked with GTP, UTP, CTP, and ddATP 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
2.65	53.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.184	α = 90
b = 153.474	β = 90
c = 230.825	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		2017-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97910	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	5.395	49	99	0.995	6.93	5.9		16580

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	5.4	5.72	95.4		0.157	0.47	5.8

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	5.4	48.988	16477	771	98.323	0.317	0.3142	0.3622	0	279.166

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]
-0.093			0.844		-0.751

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.506
r_lrange_it	27.793
r_lrange_other	27.786
r_dihedral_angle_3_deg	19.424
r_dihedral_angle_4_deg	16.444
r_mcangle_it	10.054
r_mcangle_other	10.053
r_scangle_it	7.073
r_scangle_other	7.022
r_dihedral_angle_1_deg	6.546
r_mcbond_it	5.505
r_mcbond_other	5.505
r_scbond_it	3.665
r_scbond_other	3.639
r_angle_refined_deg	1.383
r_angle_other_deg	0.715
r_symmetry_xyhbond_nbd_refined	0.347
r_nbd_other	0.346
r_symmetry_nbd_refined	0.325
r_xyhbond_nbd_refined	0.262
r_symmetry_nbd_other	0.232
r_xyhbond_nbd_other	0.225
r_nbd_refined	0.222
r_symmetry_xyhbond_nbd_other	0.219
r_nbtor_refined	0.155
r_ncsr_local_group_1	0.131
r_metal_ion_refined	0.113
r_chiral_restr	0.061
r_gen_planes_refined	0.048
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	27525
Nucleic Acid Atoms	1407
Solvent Atoms
Heterogen Atoms	33

Software

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