4I25 | pdb_00004i25

2.00 Angstroms X-ray crystal structure of NAD- and substrate-bound 2-aminomuconate 6-semialdehyde dehydrogenase from Pseudomonas fluorescens

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2D4E	PDB entry 2D4E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9.1	291	0.2 M Sodium phosphate dibasic dihydrate, 20% w/v Polyethylene glycol 3,350 , pH 9.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.253	α = 90
b = 142.932	β = 90
c = 175.125	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		2012-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.8	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	2	35	100	0.12	34	14.4	149047	149047			26.67

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	2	2.03	100

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 2D4E	2	27.22	147418	7401	98.6	0.1645	0.1622	0.1676	0.2081	0.2113	RANDOM	29.3828

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]
-0.52			-0.87		1.39

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_2_deg	35.61
f_dihedral_angle_4_deg	20.388
f_dihedral_angle_3_deg	13.558
f_dihedral_angle_1_deg	6.162
f_angle_refined_deg	1.81
f_angle_other_deg	0.917
f_chiral_restr	0.118
f_bond_refined_d	0.019
f_gen_planes_refined	0.009
f_bond_other_d	0.001
f_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14684
Nucleic Acid Atoms
Solvent Atoms	1397
Heterogen Atoms	220

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing