3DMU

Crystal structure of Staphylococcal nuclease variant PHS T62K at cryogenic temperature

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	44% MPD, 25 mM Potassium Phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.22	α = 90
b = 48.22	β = 90
c = 63.28	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	BRUKER APEX II	multi-layer optics	2005-01-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	OTHER	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	1.75	17.98	99.8	0.0301	0.0199	30.16	10.6	14741	14710			33.1

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)
	1.75	1.84	99.3		0.2839	0.2574	4.05	3.43	2016

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	1EY8.PDB	1.8	17	13483	12753	1272	94.61	0.23	0.203	0.198	0.255	RANDOM	27.909

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	29.248
r_dihedral_angle_4_deg	20.903
r_dihedral_angle_3_deg	18.093
r_dihedral_angle_1_deg	7.47
r_scangle_it	7.239
r_scbond_it	5.07
r_mcangle_it	3.159
r_angle_refined_deg	2.08
r_mcbond_it	2.056
r_chiral_restr	0.157

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.248
r_dihedral_angle_4_deg	20.903
r_dihedral_angle_3_deg	18.093
r_dihedral_angle_1_deg	7.47
r_scangle_it	7.239
r_scbond_it	5.07
r_mcangle_it	3.159
r_angle_refined_deg	2.08
r_mcbond_it	2.056
r_chiral_restr	0.157
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1024
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms	5

Software

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

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.