8RKQ

Structure of human DELTA-1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE (ALDH4A1) complexed with the molecular tweezer CLR01

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3V9G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	0.2M ammonium citrate, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 148.752	α = 90
b = 148.752	β = 90
c = 189.957	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2017-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.97794	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	2.6	48.69	99.5	0.131	0.139	0.998	9.25	8.99		72820			80.073

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.67	97.8		2.249	2.397	0.603	0.97	8.321

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.6	48.69	70717	2101	99.48	0.232	0.2307	0.2774	RANDOM	86.127

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]
2.29	1.15		2.29		-7.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.466
r_dihedral_angle_3_deg	17.649
r_dihedral_angle_4_deg	16.288
r_dihedral_angle_1_deg	6.741
r_mcangle_it	2.408
r_mcbond_it	1.394
r_mcbond_other	1.394
r_angle_refined_deg	1.232
r_angle_other_deg	1.099
r_chiral_restr	0.046

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.466
r_dihedral_angle_3_deg	17.649
r_dihedral_angle_4_deg	16.288
r_dihedral_angle_1_deg	6.741
r_mcangle_it	2.408
r_mcbond_it	1.394
r_mcbond_other	1.394
r_angle_refined_deg	1.232
r_angle_other_deg	1.099
r_chiral_restr	0.046
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16829
Nucleic Acid Atoms
Solvent Atoms	55
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	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.