3HZX | pdb_00003hzx

Crystal Structure of Staphylococcal nuclease variant D+PHS/V66K at pH 9 determined at 100 K

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BDC	3BDC (SNase D+PHS), with residues 66 and 113-116 truncated to Ala, all waters, Ca2+ and THP removed, and all b-factors truncated to 20.00A^2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	277	39 % MPD, 25 mM Potassium phosphate, pdTp, CaCl2, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.051	α = 90
b = 60.439	β = 94.61
c = 37.459	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	2009-04-21	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)	R Sym 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	2	37.34	99.8	0.0283	0.0646	27.91	14.24	9409	9409			30.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.1	100		0.172	0.2818	5.55	7.42	1280

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3BDC (SNase D+PHS), with residues 66 and 113-116 truncated to Ala, all waters, Ca2+ and THP removed, and all b-factors truncated to 20.00A^2	2	37.338	9409	9408	449	99.98	0.181	0.181	0.178	0.18	0.237	RANDOM	23.594

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]
-0.04		0.02			0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.564
r_dihedral_angle_3_deg	17.192
r_dihedral_angle_4_deg	11.361
r_dihedral_angle_1_deg	6.614
r_scangle_it	5.277
r_scbond_it	3.409
r_mcangle_it	2.229
r_angle_refined_deg	1.492
r_mcbond_it	1.319
r_chiral_restr	0.144

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.564
r_dihedral_angle_3_deg	17.192
r_dihedral_angle_4_deg	11.361
r_dihedral_angle_1_deg	6.614
r_scangle_it	5.277
r_scbond_it	3.409
r_mcangle_it	2.229
r_angle_refined_deg	1.492
r_mcbond_it	1.319
r_chiral_restr	0.144
r_bond_refined_d	0.014
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1035
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	26

Software

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