8GY0 | pdb_00008gy0

Agrocybe pediades linalool sunthase (Ap.LS)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PS1	1ps1, 2wbu
experimental model	PDB	2WBU	1ps1, 2wbu

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	295.15	10mM MgCl2, 0.2 M Sodium citrate tribasic dihydrate pH 5.6, 2% v/v Tacsimate pH 5 and 18% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.925	α = 90
b = 80.665	β = 96.05
c = 69.906	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 EIGER X 16M		2021-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97918	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.98	50	90.5	0.089	29.7	5.8		48065

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.98	2.01			0.9

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	MAD	FREE R-VALUE	1ps1, 2wbu	1.988	46.804	44039	1831	82.681	0.217	0.2144	0.22	0.2745	0.28	66.281

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]
3.179		0.546	-6.036		2.682

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.4
r_dihedral_angle_3_deg	19.269
r_dihedral_angle_4_deg	17.85
r_lrange_other	11.69
r_lrange_it	11.68
r_scangle_it	8.904
r_scangle_other	8.903
r_mcangle_other	8.682
r_mcangle_it	8.681
r_mcbond_it	6.171
r_mcbond_other	6.168
r_scbond_it	6.093
r_scbond_other	6.092
r_dihedral_angle_1_deg	5.734
r_angle_refined_deg	1.448
r_angle_other_deg	1.299
r_xyhbond_nbd_refined	0.259
r_nbd_other	0.246
r_symmetry_xyhbond_nbd_refined	0.23
r_nbd_refined	0.208
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.177
r_symmetry_nbd_refined	0.13
r_symmetry_xyhbond_nbd_other	0.12
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.068
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5049
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MADSYS	phasing