4KY7 | pdb_00004ky7

Crystal structure of Staphylococcal nuclease variant Delta+PHS V74D 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	20% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.895	α = 90
b = 60.521	β = 90
c = 75.061	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	multi-layer optics	2013-03-03	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	1.55	50	99.9	0.0165	42.83	16.24	21236	21236			19.3

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	1.55	1.65	99.3		0.089	10.58	10.41	3593

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	PDB ENTRY 3BDC	1.55	30.26	21181	21181	1090	99.86	0.1804	0.1804	0.179	0.18	0.2068	0.21	RANDOM	12.6163

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]
0.02			0.03		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.386
r_dihedral_angle_3_deg	14.947
r_dihedral_angle_4_deg	8.049
r_dihedral_angle_1_deg	6.485
r_angle_refined_deg	2.3
r_chiral_restr	0.156
r_bond_refined_d	0.021
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1061
Nucleic Acid Atoms
Solvent Atoms	132
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
APEX	data collection
APEX	data reduction
PHASER	phasing

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.