6UTX | pdb_00006utx

E. coli sigma-S transcription initiation complex with an empty bubble ("Old" 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
2.66	53.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.069	α = 90
b = 153.3	β = 90
c = 230.897	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		2017-08-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97920	APS	24-ID-C

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	4.05	48.942	99.3	0.998	8.19	5.6		38603

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	4.05	4.29	97.1		0.181	0.56	5.65

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	4.05	48.9	38450	1841	98.889	0.283	0.2792	0.3495	247.661

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]
0.192			0.367		-0.559

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	24.455
r_lrange_other	24.454
r_dihedral_angle_2_deg	19.564
r_dihedral_angle_3_deg	16.086
r_dihedral_angle_4_deg	13.496
r_mcangle_it	12.227
r_mcangle_other	12.227
r_scangle_it	9.618
r_scangle_other	9.618
r_mcbond_it	7.067
r_mcbond_other	7.066
r_dihedral_angle_1_deg	5.74
r_scbond_it	5.241
r_scbond_other	5.241
r_angle_refined_deg	1.232
r_xyhbond_nbd_other	0.643
r_angle_other_deg	0.58
r_symmetry_xyhbond_nbd_refined	0.546
r_symmetry_nbd_refined	0.37
r_nbd_other	0.36
r_xyhbond_nbd_refined	0.233
r_symmetry_nbd_other	0.209
r_nbd_refined	0.208
r_nbtor_refined	0.163
r_symmetry_xyhbond_nbd_other	0.151
r_ncsr_local_group_1	0.103
r_gen_planes_refined	0.049
r_chiral_restr	0.047
r_gen_planes_other	0.044
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	3

Software

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