4ZUI | pdb_00004zui

Crystal structure of Staphylococcal nuclease variant Delta+PHS V23H 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	30% MPD, 25 mM potassium phosphate, calcium chloride, pdTp

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.096	α = 90
b = 60.419	β = 94.41
c = 38.079	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	2015-04-15	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	99.9	0.0251	29.44	13.21	15518	15518

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		0.1722	5.34	7.28

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	32.15	14717	775	99.8	0.213	0.211	0.22	0.2503	0.25	RANDOM	18.302

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]
-0.1		0.03	-0.1		0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.82
r_dihedral_angle_3_deg	20.637
r_dihedral_angle_4_deg	17.355
r_dihedral_angle_1_deg	7.043
r_angle_refined_deg	1.827
r_angle_other_deg	0.823
r_chiral_restr	0.122
r_bond_refined_d	0.017
r_gen_planes_refined	0.011
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.82
r_dihedral_angle_3_deg	20.637
r_dihedral_angle_4_deg	17.355
r_dihedral_angle_1_deg	7.043
r_angle_refined_deg	1.827
r_angle_other_deg	0.823
r_chiral_restr	0.122
r_bond_refined_d	0.017
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1036
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	26

Software

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

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.