7PQ0 | pdb_00007pq0

Crystal structure of the Burkholderia Lethal Factor 1 (BLF1) C94S inactive mutant in complex with human eIF4A - Crystal form B

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3TUA	3TUA, 2ZU6, 2G9N
experimental model	PDB	2ZU6	3TUA, 2ZU6, 2G9N
experimental model	PDB	2G9N	3TUA, 2ZU6, 2G9N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	290	0.1 M HEPES, 4 % (w/v) PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
4.38	71.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 199.53	α = 90
b = 199.53	β = 90
c = 51.34	γ = 120

Symmetry
Space Group	P 63

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		2015-10-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	65.31	99.7	0.041	0.044	0.015	0.999	34.9	8.4		23808

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.08	97.9		0.216	0.23	0.078	0.988		8.4

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3TUA, 2ZU6, 2G9N	3	65.31	22590	1208	99.66	0.1883	0.186	0.19	0.2298	0.23	RANDOM	95.016

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]
0.53	0.26		0.53		-1.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.506
r_dihedral_angle_4_deg	15.413
r_dihedral_angle_3_deg	15.034
r_dihedral_angle_1_deg	4.366
r_angle_refined_deg	1.551
r_angle_other_deg	0.949
r_chiral_restr	0.073
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.506
r_dihedral_angle_4_deg	15.413
r_dihedral_angle_3_deg	15.034
r_dihedral_angle_1_deg	4.366
r_angle_refined_deg	1.551
r_angle_other_deg	0.949
r_chiral_restr	0.073
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4716
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.