7JWS | pdb_00007jws

Crystal structure of human ALDH1A1 bound to compound (R)-28

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6DUM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.4	293	100 mM sodium BisTris, pH 6.4, 9% PEG3350, 200 mM NaCl, and 5-10 mM YbCl3, 250 uM (R)-1-methyl-5-phenyl-6-((1-phenylethyl)thio)-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one, 1% v/v DMSO

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.065	α = 90
b = 109.065	β = 90
c = 83.126	γ = 90

Symmetry
Space Group	P 4 2 2

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	ADSC QUANTUM 210r		2017-03-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.98	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.6	109.07	99.4	0.081	0.086	0.027	11.7	9.3		66172

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63	93.5		0.671	0.731	0.285	0.85	2.3	5.9

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6DUM	1.6	109.07	62765	3350	99.35	0.2229	0.2216	0.2473	0.2639	RANDOM	30.561

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]
-1.96			-1.96		3.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.922
r_dihedral_angle_4_deg	18.145
r_dihedral_angle_3_deg	13.983
r_dihedral_angle_1_deg	6.034
r_angle_refined_deg	1.285
r_angle_other_deg	0.918
r_chiral_restr	0.072
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3814
Nucleic Acid Atoms
Solvent Atoms	465
Heterogen Atoms	29

Software

Software
Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing