7VUD | pdb_00007vud

Carotenoid Cleavage Dioxygenase 1 from Osmanthus fragrans

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NPE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	293.15	0.1M Tris pH 7.5, 1.5M Ammonium Sulfate

Crystal Properties
Matthews coefficient	Solvent content
6.09	79.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 209.941	α = 90
b = 209.941	β = 90
c = 209.941	γ = 90

Symmetry
Space Group	P 41 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	98.15	CCD	ADSC QUANTUM 210r		2021-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.98	Australian Synchrotron	MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.8	49.53	100	0.0148	0.996	10.8	81		39479

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.91			0.32	0.38	1.1

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	MOLECULAR REPLACEMENT	FREE R-VALUE	3npe	2.8	49.48	39400	1971	99.964	0.229	0.2273	0.23	0.2584	0.26	59.231

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.31
r_dihedral_angle_3_deg	22.615
r_dihedral_angle_4_deg	20.997
r_dihedral_angle_1_deg	7.634
r_lrange_other	5.362
r_lrange_it	5.352
r_scangle_other	3.827
r_scangle_it	3.795
r_mcangle_it	3.181
r_mcangle_other	3.181
r_scbond_it	2.355
r_scbond_other	2.34
r_mcbond_other	1.923
r_mcbond_it	1.922
r_angle_refined_deg	1.451
r_angle_other_deg	1.39
r_symmetry_nbd_refined	0.466
r_nbd_other	0.443
r_symmetry_nbd_other	0.219
r_nbd_refined	0.206
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.154
r_symmetry_xyhbond_nbd_other	0.107
r_symmetry_nbtor_other	0.09
r_symmetry_xyhbond_nbd_refined	0.09
r_chiral_restr	0.068
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4261
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms	83

Software

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