3C1F | pdb_00003c1f

Crystal structure of Staphylococcal nuclease variant Delta+PHS V104K at cryogenic temperature

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TQO	1TQO.PDB where all waters removed, all Bs=20.0 A^2, V104A, and E92A

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 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.079	α = 90
b = 60.518	β = 93.064
c = 38.22	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	BRUKER APEX II	multi-layer optics	2007-06-20	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	21.88	100	0.0761	0.0364	19.51	13.42	9648	9646			34.2

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		0.4489	0.3477	2.8	6.29	1307

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	1TQO.PDB where all waters removed, all Bs=20.0 A^2, V104A, and E92A	2	21.88	9617	8525	853	88.65	0.211	0.216	0.211	0.21	0.261	0.26	RANDOM	29.683

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		0.02	-0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.912
r_dihedral_angle_4_deg	17.661
r_dihedral_angle_3_deg	15.809
r_dihedral_angle_1_deg	6.148
r_scangle_it	3.336
r_scbond_it	2.157
r_angle_refined_deg	1.914
r_mcangle_it	1.497
r_mcbond_it	0.912
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.912
r_dihedral_angle_4_deg	17.661
r_dihedral_angle_3_deg	15.809
r_dihedral_angle_1_deg	6.148
r_scangle_it	3.336
r_scbond_it	2.157
r_angle_refined_deg	1.914
r_mcangle_it	1.497
r_mcbond_it	0.912
r_nbtor_refined	0.308
r_nbd_refined	0.217
r_xyhbond_nbd_refined	0.178
r_symmetry_hbond_refined	0.177
r_symmetry_vdw_refined	0.169
r_chiral_restr	0.11
r_bond_refined_d	0.015
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1041
Nucleic Acid Atoms
Solvent Atoms	54
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.