7Q9Z | pdb_00007q9z

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4AH3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		291	12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v (RS)-2-methyl-2,4-pentanediol (MPD) 0.03M of each of sodium nitrate, disodium hydrogen phosphate and ammonium sulfate in 0.1M MES/imidazole pH6.5 buffer.5 mM PLP and 5 mM pyruvate

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.15	α = 71.3
b = 60.72	β = 75.94
c = 61.8	γ = 85.73

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	PIXEL	DECTRIS EIGER2 X 16M		2021-03-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	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	1.95	56.41	97.8	0.998	8.8	3.6		55363

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	1.95	1.98			0.322

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4ah3	1.95	56.408	55310	2758	97.678	0.245	0.2433	0.24	0.2788	0.28	64.113

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]
-1.362	-2.605	5.517	-0.053	-3.352	1.164

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.666
r_dihedral_angle_3_deg	16.843
r_dihedral_angle_4_deg	16.676
r_lrange_it	12.008
r_dihedral_angle_1_deg	6.646
r_scangle_it	6.011
r_mcangle_it	5.989
r_scbond_it	3.969
r_mcbond_it	3.932
r_angle_refined_deg	1.156
r_nbtor_refined	0.31
r_metal_ion_refined	0.23
r_nbd_refined	0.218
r_symmetry_xyhbond_nbd_refined	0.205
r_symmetry_nbd_refined	0.195
r_xyhbond_nbd_refined	0.165
r_chiral_restr	0.088
r_ncsr_local_group_1	0.076
r_bond_refined_d	0.005
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6702
Nucleic Acid Atoms
Solvent Atoms	76
Heterogen Atoms	65

Software

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