3C1E

Crystal structure of Staphylococcal nuclease variant Delta+PHS L125K at cryogenic temperature

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	277	32% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 9.0, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.075	α = 90
b = 60.453	β = 93.102
c = 38.144	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	BRUKER APEX II	multi-layer optics	2008-01-10	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	1.9	38.09	99.9	0.0364	0.0215	38.45	11.09	11209	11202			27.4

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)
	1.9	2	99.8		0.1709	0.1616	6.05	3.9	1602

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	1TQO.PDB	1.9	27.61	11209	10635	1038	95.07	0.216	0.201	0.195	0.253	RANDOM	21.191

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]
		-0.01	0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.047
r_dihedral_angle_3_deg	14.633
r_dihedral_angle_4_deg	10.454
r_dihedral_angle_1_deg	5.729
r_scangle_it	3.169
r_scbond_it	2.034
r_mcangle_it	1.453
r_angle_refined_deg	1.434
r_mcbond_it	0.896
r_nbtor_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.047
r_dihedral_angle_3_deg	14.633
r_dihedral_angle_4_deg	10.454
r_dihedral_angle_1_deg	5.729
r_scangle_it	3.169
r_scbond_it	2.034
r_mcangle_it	1.453
r_angle_refined_deg	1.434
r_mcbond_it	0.896
r_nbtor_refined	0.307
r_nbd_refined	0.198
r_xyhbond_nbd_refined	0.141
r_symmetry_hbond_refined	0.141
r_symmetry_vdw_refined	0.14
r_chiral_restr	0.101
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1059
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms	26

Software

Software
Software Name	Purpose
SAINT	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
APEX	data collection
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 R01GM133198.