7VB6 | pdb_00007vb6

Crystal structure of hydroxynitrile lyase from Linum usitatissium complexed with (R)-2-hydroxy-2-methylbutanenitrile

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7VB3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293.15	0.1 M BIS-TRIS, pH 6.5, 20% w/v polyethylene glycol monomethyl ether 5000

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.178	α = 90
b = 52.103	β = 94.8
c = 169.85	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU		2020-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.542

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.723	169.255	97	0.113	0.123	0.049	9.9	6.2	168508	168508

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.723	1.82	84.7		0.663	0.663	0.723	0.284	1.1	6.2

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7VB3	1.74	49.85	159549	8653	98.59	0.1654	0.1633	0.17	0.2056	0.21	RANDOM	22.148

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]
-1.76		0.15	0.38		1.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.387
r_dihedral_angle_3_deg	13.169
r_dihedral_angle_4_deg	11.161
r_dihedral_angle_1_deg	7.229
r_angle_refined_deg	1.635
r_angle_other_deg	1.37
r_chiral_restr	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.387
r_dihedral_angle_3_deg	13.169
r_dihedral_angle_4_deg	11.161
r_dihedral_angle_1_deg	7.229
r_angle_refined_deg	1.635
r_angle_other_deg	1.37
r_chiral_restr	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12454
Nucleic Acid Atoms
Solvent Atoms	1422
Heterogen Atoms	328

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
Coot	model building
MOSFLM	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.