4OFC | pdb_00004ofc

2.0 Angstroms X-ray crystal structure of human 2-amino-3-carboxymuconate-6-semialdehye decarboxylase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4IH3	pdb entry 4IH3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	0.1 M Bis-Tris, 22% PEG 3350, 0.2 M lithium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.704	α = 90
b = 101.082	β = 90
c = 232.82	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	CCD	MARMOSAIC 300 mm CCD		2013-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

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	1.99	45	87.6	0.153		10.1	150018	131416

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.99	2.03	81.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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 4IH3	1.99	27.106	1.34	150601	130135	6186	86.41	0.1988	0.1966	0.19	0.2407	0.24	Random	29.88

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]
2.6733			0.8304		-3.5037

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.64
f_angle_d	1.155
f_chiral_restr	0.077
f_bond_d	0.008
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15984
Nucleic Acid Atoms
Solvent Atoms	994
Heterogen Atoms	6

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
DENZO	data reduction
MOLREP	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.