3NP8 | pdb_00003np8

Crystal structure of Staphylococcal nuclease variant Delta+PHS L36A at cryogenic temperature

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BDC	3BDC with all H2Os, Ca2+ and THP removed and the following truncations: H8A, T13A, L36A, Q30A, K64A, T82A, Y113A, V114A, Y115A; all b-factors were reset to 20 A^2.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	20% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 6.0, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.011	α = 90
b = 60.404	β = 93.77
c = 38.275	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	ADSC QUANTUM 315		2010-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.1000	NSLS	X25

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	98.9	0.04	21.9	7.1	15463	15463			36.9

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	1.73	92.6		0.253		6.1	736

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 (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	3BDC with all H2Os, Ca2+ and THP removed and the following truncations: H8A, T13A, L36A, Q30A, K64A, T82A, Y113A, V114A, Y115A; all b-factors were reset to 20 A^2.	1.7	30.94	15410	1540	98.95	0.1894	0.1933	0.1894	0.19	0.2296	0.23	RANDOM	34.2096

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]
-1.5		0.7	-1.32		2.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.862
r_dihedral_angle_3_deg	18.194
r_dihedral_angle_4_deg	6.858
r_dihedral_angle_1_deg	6.589
r_scangle_it	4.43
r_scbond_it	3.332
r_mcangle_it	1.977
r_angle_refined_deg	1.677
r_mcbond_it	1.353
r_chiral_restr	0.128

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.862
r_dihedral_angle_3_deg	18.194
r_dihedral_angle_4_deg	6.858
r_dihedral_angle_1_deg	6.589
r_scangle_it	4.43
r_scbond_it	3.332
r_mcangle_it	1.977
r_angle_refined_deg	1.677
r_mcbond_it	1.353
r_chiral_restr	0.128
r_bond_refined_d	0.017
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1030
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	26

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	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.