2PYK

Crystal structure of Staphylococcal nuclease variant V66Q/P117G/H124L/S128A at room temperature

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	277	37% MPD, 0.025 M potassium phosphate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.967	α = 90
b = 48.967	β = 90
c = 63.773	γ = 90

Symmetry
Space Group	P 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	CCD	APEX II CCD		2006-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	OTHER

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	50	99.4	0.0229	32.85	8.2	8881	8861

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)
	2.1	2.2	100		0.1344	7.09	4.89	1141

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-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Staphyloccocal nuclease V66E/P117G/H124L/S128A variant (at 100K), with b-factors set to 20.0 A^2 and residue 66 truncated to Ala, waters excluded	2.1	50	8810	8810	938	99.4	0.203	0.203	0.186	0.23	random	30.354

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]
-2.945			-2.945		5.89

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	3.895
c_scbond_it	2.573
c_mcangle_it	2.142
c_mcbond_it	1.413

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1039
Nucleic Acid Atoms
Solvent Atoms	38
Heterogen Atoms

Software

Software
Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
APEX	data collection
APEX	data reduction
CNS	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.