6AMF | pdb_00006amf

Crystal structure of Staphylococcal nuclease variant Delta+PHS V23K/L36E 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	7	277	24% MPD, 25 mM potassium phosphate, calcium chloride, pdTp

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.14	α = 90
b = 60.316	β = 94.32
c = 38.567	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	110	CCD	AGILENT ATLAS CCD		2017-07-27	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	1.85	38.46	99.9	0.028	35.27	9.7		12204			27.2

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	1.85	1.92	100		0.167	4.66	7

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 (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	1.85	38.46	11636	553	99.88	0.2111	0.2086	0.21	0.2605	0.26	RANDOM	23.709

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]
-0.03		0.01			0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.332
r_dihedral_angle_3_deg	15.065
r_dihedral_angle_4_deg	8.218
r_dihedral_angle_1_deg	5.654
r_angle_refined_deg	1.832
r_angle_other_deg	0.995
r_chiral_restr	0.097
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.332
r_dihedral_angle_3_deg	15.065
r_dihedral_angle_4_deg	8.218
r_dihedral_angle_1_deg	5.654
r_angle_refined_deg	1.832
r_angle_other_deg	0.995
r_chiral_restr	0.097
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1036
Nucleic Acid Atoms
Solvent Atoms	76
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
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.