5HGT

Crystal structure of Staphylococcal nuclease variant Delta+PHS L25K/I92T at cryogenic temperature

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	30% MPD, 25 mM potassium phosphate, calcium chloride, pdTp

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.024	α = 90
b = 60.424	β = 93.76
c = 37.891	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	APEX II CCD	mirrors	2013-11-11	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	1.75	50	100	0.0216	31.33	12.06	14161	14161			26.26

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	1.75	1.78	100		0.1839	5.08	5.81

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	1.75	37.81	13421	722	99.99	0.1756	0.1735	0.2124	RANDOM	21.188

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]
-0.68		0.45	-1.1		1.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.426
r_dihedral_angle_3_deg	17.367
r_dihedral_angle_4_deg	10.071
r_dihedral_angle_1_deg	6.742
r_scbond_it	2.098
r_mcangle_it	1.832
r_angle_refined_deg	1.815
r_mcbond_it	1.284
r_chiral_restr	0.187
r_bond_refined_d	0.017

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.426
r_dihedral_angle_3_deg	17.367
r_dihedral_angle_4_deg	10.071
r_dihedral_angle_1_deg	6.742
r_scbond_it	2.098
r_mcangle_it	1.832
r_angle_refined_deg	1.815
r_mcbond_it	1.284
r_chiral_restr	0.187
r_bond_refined_d	0.017
r_gen_planes_refined	0.017

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1033
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	26

Software

Software
Software Name	Purpose
APEX 2	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
APEX 2	data reduction
Coot	model building

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.