4OL7 | pdb_00004ol7

Crystal structure of Staphylococcal nuclease variant Delta+PHS V66E A109E 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	6	277	30% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.145	α = 90
b = 54.159	β = 90
c = 108.125	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	2013-10-13	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	1.67	50	99.8	0.0257	29.33	13.02	32967	32967			22.1

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	1.67	1.69	100		0.2281	4.37	5.57	1147

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	1.67	48.47	32906	32906	1669	99.97	0.1593	0.1593	0.1576	0.17	0.1907	0.2	RANDOM	14.816

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]
0.59			-0.09		-0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.511
r_dihedral_angle_4_deg	18.061
r_dihedral_angle_3_deg	14.146
r_dihedral_angle_1_deg	6.238
r_angle_refined_deg	1.798
r_mcangle_it	1.253
r_angle_other_deg	0.797
r_mcbond_it	0.779
r_mcbond_other	0.778
r_chiral_restr	0.116

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.511
r_dihedral_angle_4_deg	18.061
r_dihedral_angle_3_deg	14.146
r_dihedral_angle_1_deg	6.238
r_angle_refined_deg	1.798
r_mcangle_it	1.253
r_angle_other_deg	0.797
r_mcbond_it	0.779
r_mcbond_other	0.778
r_chiral_restr	0.116
r_bond_refined_d	0.016
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2157
Nucleic Acid Atoms
Solvent Atoms	290
Heterogen Atoms	52

Software

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

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.