5F2D | pdb_00005f2d

Crystal structure of Staphylococcal nuclease variant Delta+PHS I92N/V99T 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	PDB entry 3BDC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	277	20% MPD, 25 mM potassium phosphate, calcium chloride, pdTp

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.118	α = 90
b = 60.503	β = 93.28
c = 38.184	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	APEX II CCD	mirrors	2014-03-13	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	1.7	50	100	0.0139	48.29	25.14	15639	15639			22.76

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	1.7	1.72	100		0.1118	6.73	8.74

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	PDB entry 3BDC	1.7	38.12	14776	778	99.55	0.1917	0.1901	0.1941	0.2216	0.2277	RANDOM	18.431

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]
-1.13		0.36	-1.3		2.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.262
r_dihedral_angle_3_deg	17.774
r_dihedral_angle_4_deg	8.918
r_dihedral_angle_1_deg	6.353
r_angle_refined_deg	1.836
r_mcangle_it	1.719
r_scbond_it	1.525
r_mcbond_it	1.124
r_chiral_restr	0.144
r_gen_planes_refined	0.017
r_bond_refined_d	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1033
Nucleic Acid Atoms
Solvent Atoms	108
Heterogen Atoms	26

Software

Software
Software Name	Purpose
APEX 2	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
APEX 2	data reduction
Coot	model building