5CC4

Crystal structure of Staphylococcal nuclease variant Delta+PHS T62E/V66E at cryogenic temperature

X-RAY DIFFRACTION

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.108	α = 90
b = 60.399	β = 94.41
c = 38.013	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	2015-01-16	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	1.9	50	100	0.0274	25.61	12.67	11137	11137			26.94

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	1.9	1.93	100		0.151		8.04

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	1.9	32.12	10534	526	99.42	0.1801	0.1776	0.2268	RANDOM	24.784

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]
-0.95		0.62	-1.53		2.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.557
r_dihedral_angle_3_deg	17.178
r_dihedral_angle_4_deg	8.327
r_dihedral_angle_1_deg	7.049
r_angle_refined_deg	1.75
r_mcangle_it	1.687
r_mcbond_it	1.144
r_mcbond_other	1.092
r_angle_other_deg	0.819
r_chiral_restr	0.117

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.557
r_dihedral_angle_3_deg	17.178
r_dihedral_angle_4_deg	8.327
r_dihedral_angle_1_deg	7.049
r_angle_refined_deg	1.75
r_mcangle_it	1.687
r_mcbond_it	1.144
r_mcbond_other	1.092
r_angle_other_deg	0.819
r_chiral_restr	0.117
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1037
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms	26

Software

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

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.