4YIJ | pdb_00004yij

Crystal structure of Staphylcoccal nuclease variant Delta+PHS A109E 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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	25% MPD, 25mM potassium phosphate, calcium chloride, pdTp

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.96	α = 90
b = 54.283	β = 90
c = 108.533	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	110	CCD	APEX II CCD	mirrors	2015-01-16	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	1.64	55	99.9	0.0273	30.12	15.09	34804	34804			21.2

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	1.64	1.66	98.6		0.2227	5.34	6.38

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3bdc	1.64	54.27	33022	1723	99.87	0.1583	0.1567	0.17	0.1897	0.2	RANDOM	15.267

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]
-0.13			-0.02		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.598
r_dihedral_angle_4_deg	15.999
r_dihedral_angle_3_deg	13.276
r_dihedral_angle_1_deg	6.267
r_angle_other_deg	1.854
r_angle_refined_deg	1.807
r_mcangle_it	1.647
r_mcbond_it	1.128
r_mcbond_other	1.117
r_chiral_restr	0.121
r_bond_refined_d	0.018
r_gen_planes_refined	0.013
r_gen_planes_other	0.012
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2144
Nucleic Acid Atoms
Solvent Atoms	276
Heterogen Atoms	52

Software

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