5KGU | pdb_00005kgu

Crystal structure of Staphylococcal nuclease variant Delta+PHS N118D at cryogenic temperature

X-RAY DIFFRACTION

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	25% MPD, 25 mM potassium phosphate, calcium chloride, pdTp

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.178	α = 90
b = 60.353	β = 93.52
c = 38.425	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	AGILENT ATLAS CCD		2016-05-09	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)	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	50	99.9	0.017	56.55	10.4		11109			29.15

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	1.9	1.97	100		0.104	6.87	7.1

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	1.9	38.35	10504	590	97.94	0.1776	0.1747	0.187	0.233	0.2448	RANDOM	28.278

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]
-2.19		0.3	-1.22		3.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.979
r_dihedral_angle_3_deg	18.136
r_dihedral_angle_4_deg	10.553
r_dihedral_angle_1_deg	7.067
r_angle_refined_deg	1.88
r_mcangle_it	1.713
r_mcbond_it	1.218
r_mcbond_other	1.203
r_angle_other_deg	0.894
r_chiral_restr	0.119

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.979
r_dihedral_angle_3_deg	18.136
r_dihedral_angle_4_deg	10.553
r_dihedral_angle_1_deg	7.067
r_angle_refined_deg	1.88
r_mcangle_it	1.713
r_mcbond_it	1.218
r_mcbond_other	1.203
r_angle_other_deg	0.894
r_chiral_restr	0.119
r_bond_refined_d	0.017
r_gen_planes_refined	0.012
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1033
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms	26

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.