8S2Y | pdb_00008s2y

Crystal structure of alcohol oxidase PaAox1 from Picea abies

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JU2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298.15	0.2 M CaCl2 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.099	α = 90
b = 99.273	β = 100.249
c = 87.959	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	90	PIXEL	DECTRIS EIGER2 XE 16M		2023-01-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.64	65.24	94.6	0.119	0.05	0.997	10.5	6.3		123313

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.64	1.67	61.9		1.802	0.33

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	1.64	65.24	122933	6243	94.285	0.186	0.1851	0.185	0.2096	0.2098	29.154

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]
-0.001		0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.318
r_dihedral_angle_3_deg	12.084
r_dihedral_angle_2_deg	8.084
r_lrange_it	7.491
r_dihedral_angle_1_deg	7.041
r_scangle_it	6.274
r_scbond_it	4.173
r_mcangle_it	3.692
r_mcbond_it	2.635
r_angle_refined_deg	1.771
r_nbtor_refined	0.309
r_nbd_refined	0.202
r_symmetry_nbd_refined	0.162
r_xyhbond_nbd_refined	0.14
r_chiral_restr	0.132
r_symmetry_xyhbond_nbd_refined	0.125
r_ncsr_local_group_1	0.087
r_metal_ion_refined	0.075
r_bond_refined_d	0.01
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7437
Nucleic Acid Atoms
Solvent Atoms	764
Heterogen Atoms	271

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
xia2	data scaling
PHASER	phasing