5C3X

Crystal structure of Staphylococcal nuclease variant Delta+PHS I72D/N100E at cryogenic temperature

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BDC	PDB entry 3BDC

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
2.2	44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.126	α = 90
b = 60.173	β = 95.03
c = 38.047	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	2014-01-16	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	1.95	50	100	0.0203	36.06	23.95	10271	10271			30.35

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	1.95	1.98	100		0.1187	7.89	17.57

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	1.95	37.9	9766	494	100	0.1683	0.1662	0.2077	RANDOM	26.141

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]
-1.16		0.11	-0.09		1.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.714
r_dihedral_angle_3_deg	17.427
r_dihedral_angle_1_deg	6.526
r_dihedral_angle_4_deg	5.685
r_angle_refined_deg	1.877
r_mcangle_it	1.527
r_mcbond_it	0.989
r_mcbond_other	0.975
r_angle_other_deg	0.806
r_chiral_restr	0.106

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.714
r_dihedral_angle_3_deg	17.427
r_dihedral_angle_1_deg	6.526
r_dihedral_angle_4_deg	5.685
r_angle_refined_deg	1.877
r_mcangle_it	1.527
r_mcbond_it	0.989
r_mcbond_other	0.975
r_angle_other_deg	0.806
r_chiral_restr	0.106
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1034
Nucleic Acid Atoms
Solvent Atoms	87
Heterogen Atoms	26

Software

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

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 R01GM157729.