7X1X

Crystal Structure of cis-4,5-dihydrodiol phthalate dehydrogenase in complex with NAD+

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20% PEG3350, 0.2M AMMONIUM PHOSPHATE DIBASIC, 100mM TRIS BUFFER pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.07	α = 90
b = 92.07	β = 90
c = 163.23	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	PIXEL	DECTRIS PILATUS 6M		2021-09-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.77	46.89	99.9	0.99	12.5	1.9		21448

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.77	2.92			0.93	3.1

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3MOI	2.77	46.89	20365	1083	99.86	0.2215	0.2186	0.2779	RANDOM	58.478

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]
-1.5			4.94		-3.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.321
r_dihedral_angle_4_deg	23.708
r_dihedral_angle_3_deg	21.06
r_dihedral_angle_1_deg	7.755
r_angle_refined_deg	1.783
r_chiral_restr	0.116
r_bond_refined_d	0.008
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5256
Nucleic Acid Atoms
Solvent Atoms	149
Heterogen Atoms	106

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
Aimless	data scaling
MOLREP	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 R01GM133198.