3NXW | pdb_00003nxw

Crystal structure of Staphylococcal nuclease variant Delta+PHS L125A 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	3BDC	3BDC with all H2Os, Ca2+ and THP removed and the following truncations: H8A, T13A, Q30A, K64A, Q80, T82A, M98A, Y113A, V114A, Y115A, K116A, L125A, Q131A, K134A, K136A; all b-factors were reset to 20 A2.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	277	29% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 9.0, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.947	α = 90
b = 60.64	β = 92.54
c = 38.177	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	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	1.0000	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	1.65	50	99.4	0.057	20.3	8.2	17169	17169			35.3

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	1.65	1.68	93.9		0.207		5.2	807

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3BDC with all H2Os, Ca2+ and THP removed and the following truncations: H8A, T13A, Q30A, K64A, Q80, T82A, M98A, Y113A, V114A, Y115A, K116A, L125A, Q131A, K134A, K136A; all b-factors were reset to 20 A2.	1.65	30.92	17019	16938	1701	99.52	0.1882	0.193	0.1882	0.1877	0.2378	0.2347	RANDOM	27.946

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]
-1.47		0.28	-0.08		1.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.509
r_dihedral_angle_3_deg	15.938
r_dihedral_angle_4_deg	10.964
r_dihedral_angle_1_deg	6.044
r_scangle_it	4.448
r_scbond_it	3.103
r_mcangle_it	1.955
r_angle_refined_deg	1.633
r_mcbond_it	1.276
r_chiral_restr	0.131
r_bond_refined_d	0.017
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1030
Nucleic Acid Atoms
Solvent Atoms	54
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