7MFP | pdb_00007mfp

crystal structure of the L136 aminotransferase K185A from acanthamoeba polyphaga mimivirus in the presence of the UDP-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	7MFO

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.033	α = 90
b = 108.548	β = 90
c = 145.514	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		2019-09-19	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	1.85	50	99.8	0.084	15.4	8		123055

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	1.85	1.9	99.3		0.443	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7mfo	1.85	29.723	123059	6181	99.751	0.174	0.1718	0.18	0.2187	0.22	12.803

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]
-0.015			-0.003		0.017

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.434
r_dihedral_angle_4_deg	15.462
r_dihedral_angle_3_deg	14.713
r_dihedral_angle_1_deg	6.955
r_lrange_it	4.188
r_lrange_other	4.188
r_scangle_it	2.499
r_scangle_other	2.499
r_mcangle_it	1.684
r_mcangle_other	1.684
r_angle_refined_deg	1.613
r_scbond_it	1.547
r_scbond_other	1.547
r_angle_other_deg	1.366
r_mcbond_it	1.049
r_mcbond_other	1.048
r_metal_ion_refined	0.258
r_symmetry_nbd_refined	0.222
r_symmetry_xyhbond_nbd_refined	0.214
r_nbd_refined	0.212
r_xyhbond_nbd_refined	0.193
r_nbd_other	0.188
r_symmetry_nbd_other	0.177
r_nbtor_refined	0.172
r_symmetry_xyhbond_nbd_other	0.166
r_chiral_restr	0.079
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11213
Nucleic Acid Atoms
Solvent Atoms	1354
Heterogen Atoms	234

Software

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