1DAO

COVALENT ADDUCT OF D-AMINO ACID OXIDASE FROM PIG KIDNEY WITH 3-METHYL-2-OXO-VALERIC ACID

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.3		PROTEIN WAS CRYSTALLIZED FROM 0.5 M AMMONIUM SUCCINATE, 100 MM TRIS PH 8.3, 2 MM BENZOATE THEN SOAKED IN 20 MM 3-METHYL-2-OXO-BUTYRIC ACID

Crystal Properties
Matthews coefficient	Solvent content
3.48	60

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 326.4	α = 90
b = 136.9	β = 90
c = 196.5	γ = 90

Symmetry
Space Group	C 2 2 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	IMAGE PLATE	MARRESEARCH		1996-11-22	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11		EMBL/DESY, HAMBURG	X11

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	3.2	20	99.8	0.112	5	4		72287			30

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)
	3.2	3.25	99.1		0.352	2	4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	DENSITY AVERAGING	PDB ENTRY 1KIF	3.2	20	72287	72287	1000	99	0.232	0.232	0.232	0.26

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
t_it	7.103
t_angle_deg	3.35
t_nbd	0.12
t_bond_d	0.02
t_gen_planes	0.016
t_trig_c_planes	0.011
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21760
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms	464

Software

Software
Software Name	Purpose
DM	model building
TNT	refinement
DENZO	data reduction
SCALEPACK	data scaling
DM	phasing

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.