6RVU | pdb_00006rvu

Crystal structure of the Burkholderia Lethal Factor 1 (BLF1)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3TU8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	290	0.2 M potassium thiocyanate, 20 % (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.259	α = 90
b = 44.586	β = 90
c = 116.872	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		2017-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	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	0.99	44.58	86.7	0.078	0.084	0.032	0.996	12.6	5.8		93887

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	0.99	1.02	18.6		0.279	0.372	0.242	0.793		1.3

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	3TU8	0.99	41.69	89039	4639	86.71	0.1262	0.1251	0.1236	0.147	0.1467	RANDOM	13.399

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_rigid_bond_restr	40.395
r_dihedral_angle_2_deg	36.789
r_dihedral_angle_4_deg	23.264
r_dihedral_angle_3_deg	10.767
r_dihedral_angle_1_deg	7.241
r_angle_refined_deg	1.799
r_angle_other_deg	1.57
r_chiral_restr	0.103
r_bond_refined_d	0.014
r_gen_planes_refined	0.013
r_gen_planes_other	0.004
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1638
Nucleic Acid Atoms
Solvent Atoms	369
Heterogen Atoms	20

Software

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