Experiment: 4RKB

Crystal structure of Staphylococcal nuclease variant Delta+PHS V66T/V99T at cryogenic temperature

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BDC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	277	30% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp , pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.975	α = 90
b = 60.544	β = 93.1
c = 37.948	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	277	CCD	APEX II CCD	Multilayer	2014-01-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	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	1.88	60.54	100	0.053	26.46	11.64	11479	11479			32.6

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	2.09	2.15	100		0.198	4.17	7.58

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	3BDC	1.88	37.89	11462	11462	548	99.97	0.1874	0.1874	0.1854	0.1872	0.2253	0.2265	RANDOM	27.027

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]
-1.11		0.29	-0.43		1.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.923
r_dihedral_angle_3_deg	16.223
r_dihedral_angle_4_deg	8.328
r_dihedral_angle_1_deg	6.078
r_angle_refined_deg	1.991
r_chiral_restr	0.14
r_bond_refined_d	0.019
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1033
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms	26

Software

Software
Software Name	Purpose
XPREP	data reduction
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
APEX	data collection
APEX	data reduction