7KRG | pdb_00007krg

Crystal Structure of Mannitol Dehydrogenase (ChMDH) from Cladosporium herbarum in complex with NADP+ and Na

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	25% PEG 1500, 100 mM sodium propionate/sodium cacodylate/BIS-TRIS propane (2:1:2 molar ratio), pH 7, 5 mM NADP+

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.867	α = 90
b = 119.322	β = 94.884
c = 111.211	γ = 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	CCD	ADSC QUANTUM 315		2015-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.979	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim 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	2.0379	50	97.6	0.087	0.137	16.6	2.9		141106			27.8196736865

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	2.0379	2.09			0.656

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3GDF	2.03797368098	31.4045238396	1.3435622572	141045	1990	95.8485668076	0.154547684041	0.154135383197	0.15	0.182916664342	0.18	32.9031283964

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	4.93040445067
f_angle_d	0.828817897269
f_chiral_restr	0.0508401352847
f_bond_d	0.00703664459293
f_plane_restr	0.0041607803175

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15923
Nucleic Acid Atoms
Solvent Atoms	1414
Heterogen Atoms	388

Software

Software
Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
SBC-Collect	data collection
Coot	model building
HKL-3000	data scaling
PHASER	phasing
HKL-3000	data reduction

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.