3D6C

Crystal structure of Staphylococcal nuclease variant PHS L38E at cryogenic temperature

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	35% MPD, 25 mM Potassium Phosphate, Calcium chloride, PTP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.256	α = 90
b = 48.256	β = 90
c = 62.675	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	100	CCD	APEX II	multi-layer optics	2007-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	BRUKER	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	48.3	99.8	0.0216	0.0431	40.02	13.82	9801	9781			25.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.1	98.9		0.1097	0.1807	8.31	5.88	1323

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	2	48.28	1	9781	9740	971	99.64	0.197	0.179	0.173	0.234	RANDOM	17.646

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
r_dihedral_angle_2_deg	32.54
r_dihedral_angle_3_deg	13.887
r_dihedral_angle_4_deg	10.056
r_dihedral_angle_1_deg	5.902
r_scangle_it	3.616
r_scbond_it	2.552
r_angle_refined_deg	1.591
r_mcangle_it	1.482
r_mcbond_it	1.102
r_nbtor_refined	0.298

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.54
r_dihedral_angle_3_deg	13.887
r_dihedral_angle_4_deg	10.056
r_dihedral_angle_1_deg	5.902
r_scangle_it	3.616
r_scbond_it	2.552
r_angle_refined_deg	1.591
r_mcangle_it	1.482
r_mcbond_it	1.102
r_nbtor_refined	0.298
r_nbd_refined	0.195
r_symmetry_vdw_refined	0.143
r_xyhbond_nbd_refined	0.142
r_symmetry_hbond_refined	0.14
r_metal_ion_refined	0.111
r_chiral_restr	0.102
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1077
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms	26

Software

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

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.