9QGH | pdb_00009qgh

BV333 aminotransferase from Streptomyces sp. mutant F61C

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9GH9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		292.15	Morpheus Fusion Screen A7

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.747	α = 90
b = 176.464	β = 90
c = 111.259	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	113.15	PIXEL	DECTRIS EIGER X 16M		2024-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.852	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	1.31	88.23	94.75	0.069	1	8.9	6		221445			19.77

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.31	1.33	64.8		2.047	0.3		2.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.31	88.23	221381	2041	94.749	0.188	0.1879	0.1815	0.2102	0.2036	27.831

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]
-0.304			-0.529		0.832

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.699
r_dihedral_angle_3_deg	13.091
r_dihedral_angle_2_deg	11.447
r_lrange_it	8.059
r_scangle_it	7.671
r_dihedral_angle_1_deg	6.45
r_scbond_it	5.382
r_mcangle_it	3.607
r_mcbond_it	2.759
r_angle_refined_deg	2.411
r_nbtor_refined	0.299
r_chiral_restr	0.206
r_nbd_refined	0.193
r_xyhbond_nbd_refined	0.152
r_symmetry_nbd_refined	0.137
r_symmetry_xyhbond_nbd_refined	0.108
r_ncsr_local_group_1	0.042
r_bond_refined_d	0.019
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7044
Nucleic Acid Atoms
Solvent Atoms	601
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
XSCALE	data scaling
MoRDa	phasing