7VB3 | pdb_00007vb3

Crystal structure of hydroxynitrile lyase from Linum usitatissimum

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1D1T

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 mono methyl ether 5000

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.12	α = 90
b = 52.18	β = 95.01
c = 168.51	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	1.48	167.866	99.6	0.092	0.101	0.04	10.5	6.1		269690

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	1.482	1.56	99.2		0.661	0.661	0.72	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	1D1T	1.48	84.07	255992	13630	99.53	0.1574	0.156	0.1571	0.183	0.1846	RANDOM	17.294

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]
-1.38		0.11	0.81		0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.623
r_dihedral_angle_3_deg	11.681
r_dihedral_angle_4_deg	10.394
r_dihedral_angle_1_deg	6.941
r_angle_refined_deg	1.808
r_angle_other_deg	1.504
r_chiral_restr	0.1
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12462
Nucleic Acid Atoms
Solvent Atoms	1668
Heterogen Atoms	332

Software

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