7VB5 | pdb_00007vb5

Crystal structure of hydroxynitrile lyase from Linum usitatissimum complexed with acetone cyanohydrin

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
2.13	42.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.12	α = 90
b = 51.57	β = 94.67
c = 170	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	PIXEL	DECTRIS PILATUS 6M		2018-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.000	Photon Factory	BL-5A

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	1.58	169.436	100	0.121	0.133	0.053	8.9	6.2	223351	223351

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	1.58	1.67	100		1.323	1.323	1.443	0.568	0.6	6.3

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 (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	1.58	93.98	212183	11126	99.95	0.1722	0.1706	0.18	0.2046	0.22	RANDOM	23.96

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]
-2.03		0.78	1.5		0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.598
r_dihedral_angle_4_deg	13.117
r_dihedral_angle_3_deg	13.012
r_dihedral_angle_1_deg	7.134
r_angle_refined_deg	1.593
r_angle_other_deg	1.38
r_chiral_restr	0.081
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	35.598
r_dihedral_angle_4_deg	13.117
r_dihedral_angle_3_deg	13.012
r_dihedral_angle_1_deg	7.134
r_angle_refined_deg	1.593
r_angle_other_deg	1.38
r_chiral_restr	0.081
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	12532
Nucleic Acid Atoms
Solvent Atoms	1137
Heterogen Atoms	380

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.