7PK0 | pdb_00007pk0

Bovine Glycine N-Acyltransferase complexed with Benzoyl-CoA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	1 M sodium acetate, 30% v/v polyethylene glycol 300, pH 4.5

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.84	α = 90
b = 63.84	β = 90
c = 135.336	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	PIXEL	DECTRIS EIGER2 XE 16M		2020-10-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.5	46.44	99.96	0.069	0.072	0.02	1	15	13		45806

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	1.5	1.52			2.4	0.3	1.21

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 (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	AB INITIO PHASING	THROUGHOUT	1.5	46.44	43515	2291	99.95	0.1823	0.1808	0.2109	0.2168	RANDOM	31.1724

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]
0.65			0.65		-1.29

RMS Deviations
Key	Refinement Restraint Deviation
TORSION ANGLES. PERIOD 2 (DEGREES)	34.561
TORSION ANGLES. PERIOD 4 (DEGREES)	19.904
TORSION ANGLES. PERIOD 3 (DEGREES)	12.761
TORSION ANGLES. PERIOD 1 (DEGREES)	6.538
r_angle_refined_deg	1.655
r_angle_other_deg	1.408
r_chiral_restr	0.087
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2294
Nucleic Acid Atoms
Solvent Atoms	132
Heterogen Atoms	60

Software

Software
Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction