3C7A

A structural basis for substrate and stereo selectivity in octopine dehydrogenase (ODH-NADH)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	278	100 mM MES pH 7.0 and Na-citrate ranging from 1.0 to 1.2 M , VAPOR DIFFUSION, HANGING DROP, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
3.58	65.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.816	α = 90
b = 99.816	β = 90
c = 126.513	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298				2007-08-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X12	0.97854	EMBL/DESY, HAMBURG	X12

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.1	20	93	0.16		5.1	42694	39705	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	2.15	96.5		0.38	3	4.9

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	SAD	THROUGHOUT	2.1	20	35980	1891	99.57	0.23241	0.22999	0.27868	RANDOM	21.452

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]
-0.16			-0.16		0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.491
r_dihedral_angle_3_deg	12.885
r_dihedral_angle_4_deg	8.851
r_dihedral_angle_1_deg	4.196
r_angle_refined_deg	1.071
r_scangle_it	0.557
r_scbond_it	0.335
r_mcangle_it	0.319
r_nbtor_refined	0.288
r_mcbond_it	0.182
r_nbd_refined	0.152
r_chiral_restr	0.064
r_symmetry_hbond_refined	0.063
r_xyhbond_nbd_refined	0.041
r_symmetry_vdw_refined	0.038
r_bond_refined_d	0.009
r_gen_planes_refined	0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3093
Nucleic Acid Atoms
Solvent Atoms	453
Heterogen Atoms	84

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
Auto-Rickshaw	phasing