5EKK

Crystal structure of Staphylococcal nuclease variant Delta+PHS V39D/L125E at cryogenic temperature

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	30% MPD, 25 mM potassium phosphate, calcium chloride, pdTp

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.178	α = 90
b = 60.353	β = 93.52
c = 38.425	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		2015-08-20	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)	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	99.9	0.022	39.98	10.9	8250	8250			31.74

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	2.1	2.18	100		0.107	7.58	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	2.1	38.35	7808	429	98.82	0.1907	0.1879	0.2382	RANDOM	28.39

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]
-1.17		0.09	-0.95		2.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.568
r_dihedral_angle_3_deg	19.533
r_dihedral_angle_4_deg	11.406
r_dihedral_angle_1_deg	7.512
r_angle_refined_deg	1.928
r_mcangle_it	1.694
r_mcbond_it	1.153
r_mcbond_other	1.139
r_angle_other_deg	0.95
r_chiral_restr	0.123

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.568
r_dihedral_angle_3_deg	19.533
r_dihedral_angle_4_deg	11.406
r_dihedral_angle_1_deg	7.512
r_angle_refined_deg	1.928
r_mcangle_it	1.694
r_mcbond_it	1.153
r_mcbond_other	1.139
r_angle_other_deg	0.95
r_chiral_restr	0.123
r_bond_refined_d	0.018
r_gen_planes_refined	0.012
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1035
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms	26

Software

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