4MUP | pdb_00004mup

Crystal structure of Agrobacterium tumefaciens ATU3138 (EFI target 505157), apo structure

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FFI	PDB entries 2ffi,4do7, 4i6k, 4dia, 4di8
experimental model	PDB	4DO7	PDB entries 2ffi,4do7, 4i6k, 4dia, 4di8
experimental model	PDB	4I6K	PDB entries 2ffi,4do7, 4i6k, 4dia, 4di8
experimental model	PDB	4DIA	PDB entries 2ffi,4do7, 4i6k, 4dia, 4di8
experimental model	PDB	4DI8	PDB entries 2ffi,4do7, 4i6k, 4dia, 4di8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	Protein (10 mg/ml in 20 mM Tris, pH 7.9, 150 mM NaCl, 5 mM MgCl2). Reservoir (0.1 M HEPES, pH 7.5, 20% (w/v) PEG 4000, 10% (w/v) Isopropanol) (MCSG4 G11)). Cryoprotection (Reservoir+20% isopropanol), vapor diffusion, sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2	38.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.202	α = 90
b = 77.557	β = 95.49
c = 99.714	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	RAYONIX MX225HE	MIRRORS	2013-06-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	APS	31-ID

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	1.6	99.257	97.1	0.095	0.095	8.5	3.6	103208	103208			14.25

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	1.6	1.69	100		0.541	0.541	1.4	3.5	15449

Refinement

Statistics
Diffraction ID	Structure Solution 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	PDB entries 2ffi,4do7, 4i6k, 4dia, 4di8	1.6	31.598	103114	103114	5138	96.99	0.1486	0.1486	0.1469	0.15	0.1809	0.18	RANDOM	20.1631

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	12.611
f_angle_d	1.276
f_chiral_restr	0.075
f_bond_d	0.009
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6517
Nucleic Acid Atoms
Solvent Atoms	1073
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHENIX	phasing