Experiment: 4GRX

Structure of an omega-aminotransferase from Paracoccus denitrificans

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GJU	Homology model was build with MODELLER using PDB entries 3GJU, 3I5T, and 3HMU.
experimental model	PDB	3I5T	Homology model was build with MODELLER using PDB entries 3GJU, 3I5T, and 3HMU.
experimental model	PDB	3HMU	Homology model was build with MODELLER using PDB entries 3GJU, 3I5T, and 3HMU.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	25 %(w/v) PEG3350, 0.4 M NaCl, 10 mM urea, 0.1 M Tris/HCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.79	α = 90
b = 103.63	β = 98.88
c = 145.43	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	MARMOSAIC 225 mm CCD	Double Crystal	2009-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

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	2.6	20	99.5	0.095	14.31		60091	60091	-3	-3	41.039

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	2.6	2.7	99.6		0.558	2.76

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	Homology model was build with MODELLER using PDB entries 3GJU, 3I5T, and 3HMU.	2.6	19.83	60090	60090	3063	99.54	0.1809	0.1809	0.1784	0.1768	0.2274	0.2256	RANDOM	38.2066

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]
3.75		-0.03	-2.41		-1.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.648
r_dihedral_angle_4_deg	18.174
r_dihedral_angle_3_deg	16.208
r_dihedral_angle_1_deg	5.804
r_angle_refined_deg	1.3
r_chiral_restr	0.09
r_bond_refined_d	0.008
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14012
Nucleic Acid Atoms
Solvent Atoms	245
Heterogen Atoms	20

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction