8RKR

Structure of human DELTA-1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE (ALDH4A1) complexed with a monophosphate-tweezer

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	8.5	293	25% PEG 3350, 0.1M TRIS pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.11

Crystal Data

Unit Cell
Length ( ? )	Angle ( ? )
a = 71.914	�� = 90
b = 85.158	�� = 103.14
c = 85.615	�� = 90

Symmetry
Space Group	P 1 21 1

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		2017-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9188	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	1.2	48.47	99.8	0.08	0.086	0.999	11.12	6.746		312229			19.498

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	1.2	1.23	99.8		2.218	2.406	0.316	0.77	6.679

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	1.2	48.47	309005	3279	99.88	0.1656	0.1653	0.188	RANDOM	16.897

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]
0.19		0.46	0.2		-0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.86
r_dihedral_angle_4_deg	20.133
r_dihedral_angle_3_deg	12.445
r_dihedral_angle_1_deg	6.887
r_angle_refined_deg	1.796
r_mcangle_it	1.684
r_angle_other_deg	1.588
r_mcbond_it	1.176
r_mcbond_other	1.167
r_chiral_restr	0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.86
r_dihedral_angle_4_deg	20.133
r_dihedral_angle_3_deg	12.445
r_dihedral_angle_1_deg	6.887
r_angle_refined_deg	1.796
r_mcangle_it	1.684
r_angle_other_deg	1.588
r_mcbond_it	1.176
r_mcbond_other	1.167
r_chiral_restr	0.1
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8224
Nucleic Acid Atoms
Solvent Atoms	1132
Heterogen Atoms	84

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.