3PGB | pdb_00003pgb

Crystal structure of Aspergillus nidulans amine oxidase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1W7C	PDB ENTRY 1w7c

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.4	298	0.1M sodium acetate (pH 4.4), 25% w/v PEG 2000 MME, 0.2M ammonium sulfate, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 179.861	α = 90
b = 179.861	β = 90
c = 148.178	γ = 90

Symmetry
Space Group	I 4 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate	OSMIC MIRRORS	2010-04-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.446	38.44	97.4	0.254	7.1	7.7	44740	44740

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.43	2.56	82.5		0.815	0.815		7.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1w7c	2.45	38.44	42466	42466	2271	99.69	0.21291	0.21073	0.2093	0.25409	0.2494	RANDOM	17.405

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]
-0.89			-0.89		1.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.333
r_dihedral_angle_4_deg	16.652
r_dihedral_angle_3_deg	14.017
r_dihedral_angle_1_deg	6.256
r_scangle_it	1.357
r_angle_refined_deg	1.047
r_scbond_it	0.8
r_angle_other_deg	0.77
r_mcangle_it	0.532
r_mcbond_it	0.274
r_chiral_restr	0.059
r_mcbond_other	0.041
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5902
Nucleic Acid Atoms
Solvent Atoms	336
Heterogen Atoms	123

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
MOLREP	phasing