4L1O | pdb_00004l1o

Crystal structure of human ALDH3A1 with inhibitor 1-{[4-(1,3-benzodioxol-5-ylmethyl)piperazin-1-yl]methyl}-1H-indole-2,3-dione

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3SZA	PDB entry 3SZA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298.15	0.2 M Potassium Acetate, 20% PEG 3350, (3 microlitres of 3mg/ml of ALDH3A1+ 3 microlitres of mother liquor), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.257	α = 90
b = 86.396	β = 90
c = 170.225	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	IMAGE PLATE	RIGAKU RAXIS IV++	OSMIC CONFOCAL BLUE	2011-05-02	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 Merge I (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	2.3	50	90.6	0.146	0.06	16.26	3.4		37399		0.2

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)
1	2.3	2.34	88.1		0.146	6.7	2.7	2921

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 3SZA	2.3	47.95	37399	1990	95.98	0.17936	0.17686	0.18	0.22513	0.22	RANDOM	18.47

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]
-0.88			0.37		0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.161
r_dihedral_angle_3_deg	12.65
r_dihedral_angle_4_deg	10.917
r_dihedral_angle_1_deg	5.494
r_angle_refined_deg	1.089
r_angle_other_deg	0.724
r_chiral_restr	0.056
r_bond_refined_d	0.005
r_bond_other_d	0.003
r_gen_planes_refined	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.161
r_dihedral_angle_3_deg	12.65
r_dihedral_angle_4_deg	10.917
r_dihedral_angle_1_deg	5.494
r_angle_refined_deg	1.089
r_angle_other_deg	0.724
r_chiral_restr	0.056
r_bond_refined_d	0.005
r_bond_other_d	0.003
r_gen_planes_refined	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7019
Nucleic Acid Atoms
Solvent Atoms	648
Heterogen Atoms	48

Software

Software
Software Name	Purpose
HKL-3000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	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.