7MFQ | pdb_00007mfq

crystal structure of the L136 aminotransferase from acanthamoeba polyphaga mimivirus in complex with the TDP-viosamine external aldimine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7MFP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	protein incubated with 1 mM PLP and 5 MM TDP-viosamine 18-22% PEG-3350, 2% MPD, 100 mM MES

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.21	α = 90
b = 108.515	β = 90
c = 146.058	γ = 90

Symmetry
Space Group	P 21 21 21

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	Bruker PHOTON II		2019-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	BRUKER D8 QUEST	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.95	50	99.8	0.09	16.2	10.7		105900

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.05	99.7		0.411	3.5	5.1

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	7mfp	1.95	29.052	105900	5323	99.829	0.176	0.1733	0.18	0.2222	0.23	14.791

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]
-0.008			-0.001		0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.333
r_dihedral_angle_4_deg	19.747
r_dihedral_angle_3_deg	14.594
r_dihedral_angle_1_deg	7.009
r_lrange_it	4.33
r_lrange_other	4.33
r_scangle_it	2.588
r_scangle_other	2.588
r_mcangle_it	1.82
r_mcangle_other	1.82
r_scbond_it	1.586
r_scbond_other	1.586
r_angle_refined_deg	1.496
r_angle_other_deg	1.328
r_mcbond_it	1.121
r_mcbond_other	1.121
r_nbd_refined	0.209
r_nbd_other	0.191
r_xyhbond_nbd_refined	0.19
r_symmetry_nbd_other	0.182
r_symmetry_xyhbond_nbd_refined	0.179
r_nbtor_refined	0.171
r_symmetry_nbd_refined	0.134
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.072
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_symmetry_xyhbond_nbd_other	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11178
Nucleic Acid Atoms
Solvent Atoms	1236
Heterogen Atoms	226

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling
PHASER	phasing