Experiment: 4UXX

Structure of delta4-DgkA with AMPPCP in 9.9 MAG

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ZE5	PDB ENTRY 3ZE5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	5.6	277	7-10 %(V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 0.1 M SODIUM CHLORIDE, 0.1 M LITHIUM NITRATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPID CUBIC PHASE) METHOD AT 4 DEGREES CELCIUS WITH THE 9.9 MONOACYLGLYCEROL (MONOOLEIN, 9.9 MAG) AS THE HOSTING LIPID.CRYSTALS WERE SOAKED WITH 5-10 MM AMPPCP, 60 MM ZINC ACETATE BEFORE HARVESTING.

Crystal Properties
Matthews coefficient	Solvent content
3.4	63.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.94	α = 90
b = 72.94	β = 90
c = 195.76	γ = 120

Symmetry
Space Group	P 31 2 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	MARRESEARCH	MIRRORS	2012-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.03320, 1.28238	APS	23-ID-B

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	2.7	53.07	99.3	0.12	11.9	9.1		17218		-3	68.67

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	2.7	2.77	94.1		0.86	1.6	5.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 3ZE5	2.701	53.075	1.34	17165	850	99.25	0.2212	0.2191	0.2353	0.2577	0.2627	92.91

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.027
f_angle_d	0.749
f_chiral_restr	0.036
f_bond_d	0.012
f_plane_restr	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2576
Nucleic Acid Atoms
Solvent Atoms	13
Heterogen Atoms	207

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing