7Q9X

Crystal structure of Chromobacterium violaceum aminotransferase in complex with PLP-pyruvate adduct

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		290	12.5% PEG 8000 and 50 mM HEPES pH 7.5 10 mM PLP, 5 mM pyruvate

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.33	α = 103.56
b = 61.38	β = 89.38
c = 116.48	γ = 105.42

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	ADSC QUANTUM 315		2008-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9700	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	39.43	76.1	0.999	14.9	4.7		156999

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.64	23		0.861	2.5	4.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4ba4	1.6	39.43	156996	7878	76.103	0.229	0.2273	0.2612	17.71

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
r_dihedral_angle_2_deg	31.102
r_dihedral_angle_4_deg	15.685
r_dihedral_angle_3_deg	13.417
r_dihedral_angle_1_deg	6.894
r_lrange_it	6.767
r_scangle_it	2.043
r_mcangle_it	1.667
r_angle_refined_deg	1.422
r_scbond_it	1.254
r_mcbond_it	1.01
r_symmetry_nbd_refined	0.326
r_nbtor_refined	0.299
r_metal_ion_refined	0.29
r_symmetry_metal_ion_refined	0.225
r_nbd_refined	0.211
r_symmetry_xyhbond_nbd_refined	0.196
r_xyhbond_nbd_refined	0.16
r_ncsr_local_group_4	0.078
r_ncsr_local_group_1	0.071
r_ncsr_local_group_6	0.071
r_ncsr_local_group_3	0.07
r_ncsr_local_group_5	0.066
r_chiral_restr	0.06
r_ncsr_local_group_2	0.057
r_bond_refined_d	0.013
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14296
Nucleic Acid Atoms
Solvent Atoms	2031
Heterogen Atoms	213

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
DM	phasing