4IUN | pdb_00004iun

Crystal structure of Staphylococcal nuclease variant Delta+PHS R126E 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	40% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.858	α = 90
b = 59.465	β = 97.94
c = 34.462	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	100	CCD	APEX II CCD	multi-layer optics	2012-12-04	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	1.6	50	99.8	0.021	39.11	10.13	16317	16317			20.4

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	1.6	1.63	95.3		0.2199	4.49	2.55	572

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	1.6	34.13	16297	16297	825	99.77	0.1518	0.1518	0.1503	0.16	0.1789	0.19	RANDOM	14.7204

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]
0.03		0.11	0.45		-0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.264
r_dihedral_angle_3_deg	13.903
r_dihedral_angle_4_deg	10.562
r_dihedral_angle_1_deg	6.043
r_angle_refined_deg	1.942
r_angle_other_deg	0.886
r_chiral_restr	0.107
r_bond_refined_d	0.018
r_gen_planes_refined	0.012
r_gen_planes_other	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.264
r_dihedral_angle_3_deg	13.903
r_dihedral_angle_4_deg	10.562
r_dihedral_angle_1_deg	6.043
r_angle_refined_deg	1.942
r_angle_other_deg	0.886
r_chiral_restr	0.107
r_bond_refined_d	0.018
r_gen_planes_refined	0.012
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1083
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	39

Software

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

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.