7F5Q | pdb_00007f5q

The crystal structure of VyPAL2 peptide asparaginyl ligase in its active enzyme form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6IDV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	293.15	0.2 M lithium sulfate, 0.1 M sodium acetate, pH 4.5, 30% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.57	α = 90
b = 63.88	β = 90
c = 151.88	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	DECTRIS EIGER X 9M		2020-10-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32XU	0.99999	SPring-8	BL32XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.3	48.88	99.96	0.419	7.51	10.3		28255			27

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.382	100		2.141	1.32	10.4

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	6IDV	2.3	48.88	28250	1351	99.96	0.176	0.1748	0.17	0.2174	0.22	28.69

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]
-1.446			1.373		0.073

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.373
r_dihedral_angle_3_deg	13.878
r_dihedral_angle_4_deg	11.758
r_lrange_it	6.579
r_dihedral_angle_1_deg	6.302
r_scangle_it	4.924
r_scbond_it	3.18
r_mcangle_it	2.851
r_mcbond_it	1.794
r_angle_refined_deg	1.429
r_nbtor_refined	0.317
r_symmetry_nbd_refined	0.216
r_nbd_refined	0.208
r_xyhbond_nbd_refined	0.121
r_chiral_restr	0.103
r_symmetry_xyhbond_nbd_refined	0.081
r_ncsr_local_group_1	0.073
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4327
Nucleic Acid Atoms
Solvent Atoms	363
Heterogen Atoms	192

Software

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