3D8G | pdb_00003d8g

Crystal structure of Staphylococcal nuclease variant Delta+PHS I72R at cryogenic temperature

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TQO	RCSB entry 1tqo, all waters removed, b = 20.0, ILE-72 and ILE-92 truncated to ALA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	25% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTP, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.181	α = 90
b = 60.425	β = 90
c = 73.124	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	100	CCD	BRUKER APEX II	multi-layer optics	2007-06-13	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	1.99	46.6	99.7	0.0215	0.0581	42.54	20.75	10315	10279			23.7

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)
1	1.99	2.09	97.6		0.0965	0.2078	9.87	9.35	1358

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	RCSB entry 1tqo, all waters removed, b = 20.0, ILE-72 and ILE-92 truncated to ALA	1.99	1.99	10280	10218	1019	99.46	0.205	0.205	0.2	0.21	0.258	RANDOM	13.049

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]
			-0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.072
r_dihedral_angle_3_deg	12.563
r_dihedral_angle_4_deg	12.517
r_dihedral_angle_1_deg	5.647
r_scangle_it	2.248
r_scbond_it	1.419
r_angle_refined_deg	1.226
r_mcangle_it	0.951
r_mcbond_it	0.641
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.072
r_dihedral_angle_3_deg	12.563
r_dihedral_angle_4_deg	12.517
r_dihedral_angle_1_deg	5.647
r_scangle_it	2.248
r_scbond_it	1.419
r_angle_refined_deg	1.226
r_mcangle_it	0.951
r_mcbond_it	0.641
r_nbtor_refined	0.301
r_symmetry_hbond_refined	0.237
r_symmetry_vdw_refined	0.228
r_nbd_refined	0.203
r_xyhbond_nbd_refined	0.101
r_chiral_restr	0.078
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1045
Nucleic Acid Atoms
Solvent Atoms	87
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.