3SHL

Crystal structure of Staphylococcal nuclease variant Delta+PHS V74KL25A 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	8	277	30% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.2	α = 90
b = 60.449	β = 90
c = 74.142	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 315		2010-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25		NSLS	X25

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	1.47	50	99	0.059	15.4	13.3	24862	24862			25.1

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	1.47	1.5	99.4		0.374		13.5	1212

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3BDC	1.48	29.53	24816	24816	2514	98.92	0.1892	0.1861	0.2164	RANDOM	20.9597

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]
0.21			-0.86		0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.897
r_dihedral_angle_3_deg	15.949
r_dihedral_angle_4_deg	12.035
r_dihedral_angle_1_deg	6.911
r_scangle_it	4.855
r_scbond_it	3.223
r_mcangle_it	1.905
r_angle_refined_deg	1.615
r_mcbond_it	1.22
r_chiral_restr	0.126

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.897
r_dihedral_angle_3_deg	15.949
r_dihedral_angle_4_deg	12.035
r_dihedral_angle_1_deg	6.911
r_scangle_it	4.855
r_scbond_it	3.223
r_mcangle_it	1.905
r_angle_refined_deg	1.615
r_mcbond_it	1.22
r_chiral_restr	0.126
r_gen_planes_refined	0.015
r_bond_refined_d	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1032
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms	26

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	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.