6UUB | pdb_00006uub

E. coli sigma-S transcription initiation complex with a mismatching UTP ("Fresh" crystal soaked with UTP for 2 hours)

X-RAY DIFFRACTION

---

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
2.73	54.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.942	α = 90
b = 154.992	β = 90
c = 233.253	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		2017-06-09	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	3.95	38.9	99.1	0.999	9.8	5		42501

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	3.95	4.19	95.9		0.146		4.5

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5IPL	3.955	38.9	42180	2024	98.374	0.306	0.3028	0.3746	281.672

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]
-0.951			1.606		-0.655

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	32.149
r_lrange_other	32.149
r_dihedral_angle_2_deg	20.215
r_mcangle_it	18.01
r_mcangle_other	18.01
r_dihedral_angle_3_deg	16.059
r_scangle_it	14.119
r_scangle_other	14.119
r_dihedral_angle_4_deg	12.926
r_mcbond_it	10.625
r_mcbond_other	10.624
r_scbond_it	7.896
r_scbond_other	7.896
r_dihedral_angle_1_deg	5.458
r_angle_refined_deg	1.181
r_angle_other_deg	0.509
r_symmetry_nbd_refined	0.388
r_nbd_other	0.378
r_symmetry_xyhbond_nbd_refined	0.272
r_xyhbond_nbd_refined	0.233
r_symmetry_nbd_other	0.213
r_nbd_refined	0.21
r_nbtor_refined	0.162
r_symmetry_xyhbond_nbd_other	0.128
r_ncsr_local_group_1	0.113
r_gen_planes_refined	0.05
r_gen_planes_other	0.046
r_chiral_restr	0.044
r_metal_ion_refined	0.026
r_bond_refined_d	0.005
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	27482
Nucleic Acid Atoms	1356
Solvent Atoms
Heterogen Atoms	33

Software

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