1XXV | pdb_00001xxv

Yersinia YopH (residues 163-468) binds phosphonodifluoromethyl-Phe containing hexapeptide at two sites

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		YopH (residues 163-468) with bound VO4 (not submitted to PDB)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	10 mg/ml protein, 0.5 mM phosphonodifluoro-Phe-containing peptide in 1 mM imidazole. Precipitant: 22% polyethylene glycol (PEG) 4000, 8 mM MnCl2, 0.1% beta-mercaptoethanol, 100 mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.13	α = 104.45
b = 47.17	β = 115.05
c = 71.82	γ = 89.97

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	AREA DETECTOR	UCSD MARK III	monochromator		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

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	2.5	50	85.5	0.075			18319	18319

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	YopH (residues 163-468) with bound VO4 (not submitted to PDB)	2.5	50	18319	18319	892	85.5	0.178	0.229	random	22

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
c_scbond_it	2.138
c_angle_deg	1.183
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4534
Nucleic Acid Atoms
Solvent Atoms	297
Heterogen Atoms

Software

Software
Software Name	Purpose
SDMS	data collection
SDMS	data reduction
MERLOT	phasing
CNS	refinement
SDMS	data scaling

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.