7PPZ | pdb_00007ppz

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

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	290	0.1 M MES, 50 mM magnesium chloride, 10 % (w/v) 2-propanol, 5 % (w/v) PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.98	α = 90
b = 50.36	β = 111.92
c = 95.74	γ = 90

Symmetry
Space Group	C 1 2 1

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		2014-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	2.52	63.07	99.2	0.163	0.19	0.096	0.985	8.1	3.8		20378

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	2.52	2.59	98.7		0.725	0.852	0.441	0.703		3.6

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 and 2ZU6	2.52	63.07	19347	1030	98.83	0.2053	0.2016	0.21	0.2761	0.28	RANDOM	27.593

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]
-1.36		-1.42	-1.33		2.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.838
r_dihedral_angle_4_deg	13.735
r_dihedral_angle_3_deg	13.062
r_dihedral_angle_1_deg	3.759
r_angle_refined_deg	1.675
r_angle_other_deg	0.943
r_chiral_restr	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.838
r_dihedral_angle_4_deg	13.735
r_dihedral_angle_3_deg	13.062
r_dihedral_angle_1_deg	3.759
r_angle_refined_deg	1.675
r_angle_other_deg	0.943
r_chiral_restr	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4602
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
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.