4TNL | pdb_00004tnl

1.8 A resolution room temperature structure of Thermolysin recorded using an XFEL

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2TLI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		298	300 ul of the protein stock was mixed in a 1:1 ratio with 40% PEG 2000, 100 mM MES pH 6.5, 5 mM CaCl2. Crystallization occurred within minutes.

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.0407	α = 90
b = 93.0407	β = 90
c = 130.41	γ = 120

Symmetry
Space Group	P 61 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	PIXEL	CS-PAD detector	Collected at the CXI instrument at LCLS/SLAC using the CSPAD	2013-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE CXI	1.27	SLAC LCLS	CXI

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.8	34.27	100	71.7	1468		31458			16.3967395539

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.86	100			14.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2tli	1.8	34.27	1.42149651097	58500	3063	99.9128964492	0.212950766366	0.211866857775	0.22	0.232602531993	0.23	20.1244048785

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
f_dihedral_angle_d	12.5608297587
f_angle_d	0.923727439628
f_chiral_restr	0.0342922692207
f_bond_d	0.00514226974771
f_plane_restr	0.0040116139072

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2415
Nucleic Acid Atoms
Solvent Atoms	324
Heterogen Atoms	5

Software

Software
Software Name	Purpose
PHENIX	refinement
cctbx.xfel	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.