9GIP | pdb_00009gip

BFL1 covalently bound to inhibitor compound 7

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8RPO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.71	293	Protein:ligand complex at ~4mg/ml in 20 mM HEPES pH 7.5, 150 mM NaCl, 5% glycerol, 2 mM TCEP, 1%DMSO. 150nL mixed with 150nL of well solution, 0.1M PCPT* pH 8.71, Na3 Citrate 0.93 M. *PCPT = Sodium propionate, sodium cacodylate trihydrate, bis-tris propane buffer system. Using STPLabtech Mosquito.

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.883	α = 90
b = 43.033	β = 96.82
c = 43.184	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER2 X 16M		2022-01-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97950	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	1.463	39.601	68.6	0.041	0.045	0.02	0.999	14.6	4.8		17326

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	1.463	1.602	14.4		0.76	0.92	0.506	0.555	1.2	2.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.463	39.6	17326	815	68.6	0.2081	0.206	0.2012	0.2488	0.245	RANDOM	28.47

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]
1.1492		2.6248	-1.7571		0.6079

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	15.34
t_omega_torsion	2.74
t_angle_deg	0.99
t_bond_d	0.011
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1168
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	27

Software

Software
Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
autoPROC	data processing
STARANISO	data scaling
PHASER	phasing
Coot	model building

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.