9G8F | pdb_00009g8f

Carotenoid cleavage oxygenase from Moesziomyces aphidis bound to orto vanillin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	0.2M Sodium acetate trihydrate 0.1M Sodium HEPES 7.525% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.883	α = 90
b = 84.937	β = 108.399
c = 107.02	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		2023-08-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.03322	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.84	48.76	96.8	0.154	0.184	0.099	0.99	9.5	6.5		101754

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.84	1.88	60.5		0.618	0.735	0.394	0.919	4	6.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.844	48.76	101375	5064	96.338	0.212	0.2095	0.2095	0.2593	0.2593	20.601

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]
-1.085		0.903	-0.462		0.774

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.831
r_dihedral_angle_3_deg	13.668
r_dihedral_angle_2_deg	10.327
r_dihedral_angle_1_deg	7.961
r_lrange_it	6.382
r_scangle_it	4.385
r_scbond_it	3.321
r_mcangle_it	3.197
r_mcbond_it	2.476
r_angle_refined_deg	2.344
r_nbtor_refined	0.305
r_nbd_refined	0.212
r_symmetry_nbd_refined	0.207
r_xyhbond_nbd_refined	0.203
r_chiral_restr	0.164
r_symmetry_xyhbond_nbd_refined	0.129
r_ncsr_local_group_1	0.077
r_bond_refined_d	0.014
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8420
Nucleic Acid Atoms
Solvent Atoms	996
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing