9G88 | pdb_00009g88

Carotenoid cleavage oxygenase from Moesziomyces aphidis bound to acetate

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	20%w/vPolyethyleneglycol 3,350 200mM Lithiumacetate 30% GOL

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.155	α = 90
b = 85.957	β = 100.336
c = 93.87	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		2023-06-05	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	1.4	46.17	97.7	0.054	0.073	0.048	0.998	9.5	3.8		216121

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	1.4	1.42			1.005	1.325	0.851	0.432		3.1

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	1.4	46.17	215828	10853	97.547	0.169	0.1676	0.1676	0.1929	0.193	21.317

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]
-0.299		-0.363	0.555		-0.116

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.747
r_dihedral_angle_3_deg	12.682
r_dihedral_angle_2_deg	8.321
r_dihedral_angle_1_deg	7.241
r_lrange_it	5.241
r_scangle_it	4.246
r_scbond_it	2.997
r_mcangle_it	2.295
r_angle_refined_deg	1.966
r_mcbond_it	1.69
r_nbtor_refined	0.307
r_nbd_refined	0.197
r_symmetry_nbd_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.172
r_chiral_restr	0.128
r_xyhbond_nbd_refined	0.113
r_ncsr_local_group_1	0.067
r_bond_refined_d	0.012
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8420
Nucleic Acid Atoms
Solvent Atoms	1320
Heterogen Atoms	10

Software

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