6UTW | pdb_00006utw

E. coli sigma-S transcription initiation complex with a 4-nt RNA ("Fresh" crystal)

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
2.75	55.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.99	α = 90
b = 155.447	β = 90
c = 234.735	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	3.85	49.4	93.7	0.999	8.85	3.54		43708

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	3.85	4.09	90.2		0.193	0.49	3.25

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	3.854	49.396	43241	2059	92.643	0.271	0.2683	0.3293	237.76

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]
0.2			0.307		-0.507

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_other	32.191
r_lrange_it	32.19
r_dihedral_angle_2_deg	22.44
r_mcangle_it	19.397
r_mcangle_other	19.397
r_scangle_other	16.907
r_scangle_it	16.906
r_dihedral_angle_3_deg	16.588
r_dihedral_angle_4_deg	16.432
r_mcbond_it	11.81
r_mcbond_other	11.807
r_scbond_it	9.905
r_scbond_other	9.903
r_dihedral_angle_1_deg	6.112
r_angle_refined_deg	1.389
r_symmetry_xyhbond_nbd_refined	0.47
r_angle_other_deg	0.464
r_xyhbond_nbd_other	0.439
r_nbd_other	0.369
r_symmetry_nbd_refined	0.361
r_xyhbond_nbd_refined	0.227
r_symmetry_nbd_other	0.223
r_nbd_refined	0.22
r_symmetry_xyhbond_nbd_other	0.179
r_nbtor_refined	0.153
r_ncsr_local_group_1	0.149
r_chiral_restr	0.054
r_gen_planes_refined	0.054
r_gen_planes_other	0.049
r_bond_refined_d	0.006
r_bond_other_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	27572
Nucleic Acid Atoms	1493
Solvent Atoms
Heterogen Atoms	13

Software

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