9AVH | pdb_00009avh

Crystal structure of an aryl-alcohol-oxidase from Bjerkandera adusta.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5OC1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	12% v/v glycerol, 1.5 M ammonium sulfate, 0.1 mM Tris/HCl, pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.035	α = 90
b = 82.746	β = 90
c = 116.837	γ = 90

Symmetry
Space Group	P 21 21 21

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		2021-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979257	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.8	116.84	98.9	0.097	12.2	6.7		50514

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9	98.2		0.843	2.7	6.8

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	1.8	67.526	50458	2464	98.699	0.146	0.1434	0.1568	0.1883	0.1934	22.479

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]
-0.296			-1.286		1.582

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.553
r_dihedral_angle_3_deg	11.679
r_lrange_it	7.418
r_lrange_other	7.321
r_dihedral_angle_2_deg	6.812
r_dihedral_angle_1_deg	6.641
r_scangle_it	4.562
r_scangle_other	4.486
r_scbond_it	3.039
r_scbond_other	2.995
r_mcangle_other	2.464
r_mcangle_it	2.463
r_mcbond_it	1.781
r_mcbond_other	1.78
r_angle_refined_deg	1.665
r_angle_other_deg	0.569
r_nbd_other	0.253
r_nbd_refined	0.218
r_symmetry_nbd_other	0.198
r_symmetry_nbd_refined	0.196
r_symmetry_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.082
r_dihedral_angle_other_2_deg	0.037
r_gen_planes_refined	0.01
r_bond_refined_d	0.008
r_chiral_restr_other	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4407
Nucleic Acid Atoms
Solvent Atoms	366
Heterogen Atoms	124

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing