7X2Y

Crystal Structure of cis-4,5-dihydrodiol phthalate dehydrogenase in complex with NAD+ and 3-Hydroxybenzoate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M Ammonium phosphate dibasic, and 20 % polyethylene glycol 3350, 100 mM Tris buffer pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.579	α = 90
b = 88.315	β = 90
c = 162.97	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	RIGAKU HyPix-6000HE		2021-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

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	2.48	27.18	99.8	0.994	11.6	6.8		28203

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	2.48	2.54	99.8		0.904

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	2.48	27.18	26742	1412	99.69	0.1943	0.1921	0.2351	RANDOM	21.005

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]
-1.08			3.72		-2.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.851
r_dihedral_angle_4_deg	20.375
r_dihedral_angle_3_deg	18.763
r_dihedral_angle_1_deg	7.289
r_angle_refined_deg	1.643
r_chiral_restr	0.116
r_bond_refined_d	0.008
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5336
Nucleic Acid Atoms
Solvent Atoms	334
Heterogen Atoms	190

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrysalisPro	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.