5VKR

Horse liver alcohol dehydrogenase complexed with adenosine-5-diphosphoribose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8ADH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICRODIALYSIS	8.4	278	10 mg/ml protein in dialysis bag dialyzed against 50 mM Tris-HCl, pH 8.4 as the concentration of 2-methyl-2,4-pentanediol was raised to 25 %. A crystal was soaked with 2 mM adenosine-5-diphosphoribose in the final outer dialysate for 1 hr. Crystal flash vitrified by plunging it into liquid N2.

Crystal Properties
Matthews coefficient	Solvent content
2.2	44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.37	α = 90
b = 74.27	β = 90
c = 180.95	γ = 90

Symmetry
Space Group	C 2 2 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	CCD	ADSC QUANTUM 4	Si(111)	2001-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1.0093	APS	19-ID

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	1.8	20	91.7	0.117	9	7.64		30816			43.6

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)
1	1.8	1.86	84.8		0.507	2.1	5.68

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	8ADH	1.8	20	30816	1328	91.68	0.19233	0.19001	0.24775	RANDOM	50.595

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]
0.18			3.2		-3.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.311
r_dihedral_angle_4_deg	19.867
r_dihedral_angle_3_deg	16.82
r_long_range_B_refined	11.44
r_long_range_B_other	11.431
r_scangle_other	9.798
r_dihedral_angle_1_deg	6.737
r_scbond_it	6.475
r_scbond_other	6.474
r_mcangle_other	5.58
r_mcangle_it	5.564
r_mcbond_it	4.164
r_mcbond_other	4.113
r_angle_refined_deg	2.066
r_angle_other_deg	1.086
r_chiral_restr	0.123
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2785
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	38

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
AMoRE	phasing