3D4W

Crystal structure of Staphylococcal nuclease variant Delta+PHS A109R at cryogenic temperature

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TQO	PDB entry 1tqo, all waters removed, b = 20.0, ILE-92 truncated to ALA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	43% MPD, 25 mM Potassium Phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.09	α = 90
b = 59.843	β = 90
c = 73.558	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	BRUKER APEX II	multi-layer optics	2006-11-10	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	34.1	99.7	0.0196	0.0394	41.54	12.05	12416	12416			23.7

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	1.9	2	98.4		0.1077	0.188	8.46	5.91	1692

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	PDB entry 1tqo, all waters removed, b = 20.0, ILE-92 truncated to ALA	1.9	31.3	12441	12337	1215	99.16	0.197	0.197	0.191	0.252	RANDOM	16.382

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			0.03		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.123
r_dihedral_angle_3_deg	13.174
r_dihedral_angle_4_deg	8.413
r_sphericity_free	6.102
r_dihedral_angle_1_deg	6.083
r_scangle_it	3.836
r_sphericity_bonded	2.895
r_scbond_it	2.639
r_mcangle_it	1.98
r_rigid_bond_restr	1.734
r_angle_refined_deg	1.43
r_mcbond_it	1.308
r_nbtor_refined	0.302
r_nbd_refined	0.197
r_symmetry_vdw_refined	0.151
r_symmetry_hbond_refined	0.144
r_xyhbond_nbd_refined	0.125
r_chiral_restr	0.12
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1065
Nucleic Acid Atoms
Solvent Atoms	97
Heterogen Atoms	13

Software

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