5KYL

Crystal structure of Staphylococcal nuclease variant Delta+PHS T62K/V66E pH 7 at cryogenic temperature

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	30% MPD, 25 mM potassium phosphate, calcium chloride, pdTp

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.062	α = 90
b = 60.498	β = 94.28
c = 38.3	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	110	CCD	AGILENT ATLAS CCD	mirrors	2015-08-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	OTHER	1.54

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	1.85	50	100	0.02	50.97	10.1		12150			24.41

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	1.85	1.92	100		0.105	8.03	6.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3BDC	1.85	38.19	11469	665	99.93	0.1797	0.1774	0.22	RANDOM	19.315

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]
-0.02		0.01	0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.86
r_dihedral_angle_3_deg	15.49
r_dihedral_angle_4_deg	10.594
r_dihedral_angle_1_deg	6.062
r_mcangle_it	2.318
r_angle_refined_deg	1.854
r_mcbond_it	1.568
r_mcbond_other	1.546
r_angle_other_deg	0.951
r_chiral_restr	0.113

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.86
r_dihedral_angle_3_deg	15.49
r_dihedral_angle_4_deg	10.594
r_dihedral_angle_1_deg	6.062
r_mcangle_it	2.318
r_angle_refined_deg	1.854
r_mcbond_it	1.568
r_mcbond_other	1.546
r_angle_other_deg	0.951
r_chiral_restr	0.113
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1037
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	26

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data reduction
CrysalisPro	data scaling
CrysalisPro	data collection

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 R01GM133198.