4A6U | pdb_00004a6u

Crystal structure of the omega transaminase from Chromobacterium violaceum in the apo form, crystallised from PEG 3350

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4A6R	PDB ENTRY 4A6R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.4		200 NL OF PROTEIN AT 12 MG/ML MIXED WITH 200NL OF 20 % W/V PEG 3350, 0.2 M NASCN, 0.1 M HEPES PH 7.5

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.17	α = 109.14
b = 61.11	β = 85.59
c = 60.24	γ = 103.25

Symmetry
Space Group	P 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 SX-165	MULTILAYER MIRROR, VERTICALLY FOCUSING	2011-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-2		MAX II	I911-2

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	1.7	30	93.5	0.07	12.7	2.7		78926			12.34

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	1.7	1.73	72.6		0.42	3.1	2

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 4A6R	1.687	29.473	1.99	78922	3888	93.58	0.1557	0.1545	0.17	0.1799	0.19

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]
3.0967	-0.6546	-2.1588	-2.7565	1.0691	-0.3402

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.356
f_angle_d	1.116
f_chiral_restr	0.067
f_bond_d	0.008
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6154
Nucleic Acid Atoms
Solvent Atoms	617
Heterogen Atoms	11

Software

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

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.