9G89 | pdb_00009g89

Carotenoid cleavage oxygenase from Moesziomyces aphidis bound to 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	0.1MPCTP 7.0 25% w/v PEG 1500 30% GOL

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.68	α = 90
b = 84.676	β = 108.349
c = 106.571	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	1.67	48.56	98.8	0.087	0.103	0.054	0.999	12.6	6.9		137992

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)
	1.67	1.7	98.4		1.473	1.737	0.911	0.528	1.2	7

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	1.671	48.56	137923	6946	98.667	0.164	0.1629	0.1628	0.1944	0.1945	26.999

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]
-0.636		0.811	0.514		-0.342

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.962
r_dihedral_angle_3_deg	12.521
r_dihedral_angle_2_deg	8.176
r_dihedral_angle_1_deg	7.502
r_lrange_it	5.765
r_scangle_it	4.877
r_scbond_it	3.53
r_mcangle_it	3.01
r_mcbond_it	2.266
r_angle_refined_deg	1.919
r_symmetry_xyhbond_nbd_refined	0.324
r_nbtor_refined	0.306
r_symmetry_nbd_refined	0.194
r_nbd_refined	0.191
r_xyhbond_nbd_refined	0.146
r_chiral_restr	0.124
r_ncsr_local_group_1	0.062
r_gen_planes_refined	0.011
r_bond_refined_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8406
Nucleic Acid Atoms
Solvent Atoms	893
Heterogen Atoms	60

Software

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