5KLX | pdb_00005klx

Crystal Structure of SMT Fusion Peptidyl-Prolyl Cis-Trans Isomerase from Burkholderia Pseudomallei Complexed with SF110

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3UF8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	BUPSA.00130.A.D21 (CID4597, SMT TAG ON, BATCH 1264062) AT 10.37MG/ML (IN 25MM TRIS, PH8.0, 200MM NACL, 1% GLYCEROL, 1MM TCEP BUFFER) WAS INCUBATED WITH 2MM SF110_S (BSI5665). CRYSTALS WERE PRODUCED BY SITTING DROP VAPOR IFFUSION WITH AN EQUAL VOLUME COMBINATION OF THE PROTEIN/LIGAND COMPLEX AND A SOLUTION CONTAINING 10% W/V PEG20,000, 20% V/V PEG MME 550, 0.03M MGCL2, 0.03M CACL2, 0.1M MES/IMIDAZOLE, PH6.5 (MORPHEUS A1). CRYSTAL TRACKING ID 273103A1, RVA0-10, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.89	α = 90
b = 34.11	β = 115.45
c = 119.92	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	CCD	MARMOSAIC 300 mm CCD	BERYLLIUM LENSES	2016-06-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97857	APS	21-ID-G

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	2.45	50	99.4	0.075	14.99	3.7		29732		-3	47.15

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	2.45	2.51	99.7		0.569	2.26	3.8

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3uf8	2.45	37.79	29705	1486	99.5	0.201	0.198	0.2	0.256	0.26	56.54

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	15.572
f_angle_d	0.916
f_chiral_restr	0.052
f_bond_d	0.007
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5148
Nucleic Acid Atoms
Solvent Atoms	139
Heterogen Atoms	139

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
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.