Experiment: 4A72

Crystal structure of the omega transaminase from Chromobacterium violaceum in a mixture of apo and PLP-bound states

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 IN 1 MM CYCLOSERINE MIXED WITH 200 NL OF RESERVOIR CONSISTING OF 0.1 M HEPES PH 7.5, 150-300 MM NACL AND 22.5-27.5% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.35	α = 105.27
b = 62.12	β = 90.66
c = 119.24	γ = 104.43

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	MULTILAYER MIRROR, VERTICALLY FOCUSING	2011-06-06	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	2.4	30	95.5	0.1	8.5	2.3		61839			27.53

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	2.4	2.45	82.6		0.5	2.1	2.2

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	2.4	26.391	1.99	61746	3139	96.39	0.1763	0.1729	0.1763	0.2394	0.2389

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]
4.487	4.6434	2.0306	-1.734	-4.874	-2.753

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.732
f_angle_d	0.639
f_chiral_restr	0.038
f_bond_d	0.002
f_plane_restr	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13841
Nucleic Acid Atoms
Solvent Atoms	528
Heterogen Atoms	30

Software

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