5EKL | pdb_00005ekl

Crystal structure of Staphylococcal nuclease variant Delta+PHS T62D/N100E 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	7	277	21% MPD, 25 mM potassium phosphate, calcium chloride, pdTp

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.927	α = 90
b = 59.855	β = 90
c = 79.829	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	2015-07-02	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	2.1	50	100	0.042	20.71	11.52	9178	9178			24.85

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	2.1	2.13	100		0.1724	5.58	8.83

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	2.1	47.89	8689	450	99.98	0.1883	0.1854	0.1921	0.2442	0.2427	RANDOM	17.75

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]
-1.36			0.2		1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.552
r_dihedral_angle_3_deg	18.182
r_dihedral_angle_4_deg	8.741
r_dihedral_angle_1_deg	8.039
r_angle_refined_deg	1.865
r_mcangle_it	1.328
r_angle_other_deg	0.889
r_mcbond_it	0.814
r_mcbond_other	0.813
r_chiral_restr	0.112
r_bond_refined_d	0.018
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1035
Nucleic Acid Atoms
Solvent Atoms	65
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