9D04 | pdb_00009d04

CO-CRYSTAL STRUCTURE OF CIRCULARLY PERMUTED HUMAN TASPASE-1 BOUND TO LIGAND SMDC994967 1-(ETHENESULFONYL)-4-{[4- (TRIFLUOROMETHOXY)PHENYL]METHYL}PIPERAZINE

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.8	289	HUMAN TASPASE-1 VCID 11900 AT 9.23 MG/ML IN 20 MM HEPES PH 8, 0.5 M NACL, 5% GLYCEROL AGAINST PACT SCREEN CONDITION B11 CONTAINING 0.1M MES, PH 5.8, 17% PEG 6000, 0.2M CALCIUM CHLORIDE + 2.5MM 107546 (SMDC994967) SUPPLEMENTED WITH 20% ETHYLENE GLYCOL AS A CRYO-PROTECTANT, CRYSTAL TRACKING ID 282660C3, UNIQUE PUCK ID GSA4-1

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.28	α = 90
b = 60.28	β = 90
c = 318.13	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX-300		2016-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97856	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.1	30.14	99.9	0.071	17.25	5.85		38039			38.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	30.14	99.9		0.565	3.47

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	THROUGHOUT	internal structure	2.1	30.14	1.36	37912	1975	99.9	0.156	0.153	0.1551	0.198	0.1985	44.32

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4470
Nucleic Acid Atoms
Solvent Atoms	243
Heterogen Atoms	51

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

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.