3KVE | pdb_00003kve

Structure of native L-amino acid oxidase from Vipera ammodytes ammodytes: stabilization of the quaternary structure by divalent ions and structural changes in the dynamic active site

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F8R	PDB entry 1F8R

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 196.978	α = 90
b = 95.839	β = 92.53
c = 108.442	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	MAR CCD 165 mm	mirrors	2008-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8	EMBL/DESY, HAMBURG	X13

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	2.57	27.4	97.1	0.172	10.6	7.1	63563	62717	1	1	19.3

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)
	2.57	2.66	74.7		0.448		3.9	4853

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 (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 1F8R	2.57	27.4	60346	3212	98.04	0.19537	0.19105	0.19	0.27609	0.27	RANDOM	19.805

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]
1		0.11	-0.74		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.41
r_dihedral_angle_4_deg	20.408
r_dihedral_angle_3_deg	20.38
r_dihedral_angle_1_deg	7.474
r_scangle_it	2.395
r_angle_refined_deg	1.523
r_scbond_it	1.467
r_mcangle_it	1.018
r_mcbond_it	0.573
r_nbtor_refined	0.319

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.41
r_dihedral_angle_4_deg	20.408
r_dihedral_angle_3_deg	20.38
r_dihedral_angle_1_deg	7.474
r_scangle_it	2.395
r_angle_refined_deg	1.523
r_scbond_it	1.467
r_mcangle_it	1.018
r_mcbond_it	0.573
r_nbtor_refined	0.319
r_nbd_refined	0.227
r_xyhbond_nbd_refined	0.19
r_symmetry_vdw_refined	0.173
r_metal_ion_refined	0.164
r_symmetry_hbond_refined	0.138
r_chiral_restr	0.111
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15456
Nucleic Acid Atoms
Solvent Atoms	554
Heterogen Atoms	272

Software

Software
Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.