8G4V | pdb_00008g4v

Horse liver alcohol dehydrogense His-51-Gln form complexed with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DWV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICRODIALYSIS	7	278	10 mg/ml protein in 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfate buffer with 0.25 mM EDTA, 2 mM NAD+ and 15 mM 2,3,4,5,6-pentafluorobenzyl alcohol, crystals formed at ~13 % 2-methyl-2,4-pentanediol, raised to 25% MPD before crystal pliunged into liquid N2.

Crystal Properties
Matthews coefficient	Solvent content
2.28	46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.17	α = 92.02
b = 51.59	β = 102.89
c = 92.77	γ = 110.04

Symmetry
Space Group	P 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 210		2004-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.000	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.2	19.96	91.1	0.06	0.065	13.3	6.13		211946

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.24		74.4	0.181	0.212		3.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4dwv	1.2	19.96	207414	2091	89.98	0.13518	0.13493	0.14	0.1607	0.16	RANDOM	17.445

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]
0.19	-0.33	0.06	0.53	0.11	-0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.392
r_dihedral_angle_4_deg	13.729
r_dihedral_angle_3_deg	12.183
r_dihedral_angle_1_deg	6.595
r_rigid_bond_restr	4.988
r_scangle_other	3.215
r_scbond_it	3.139
r_scbond_other	3.139
r_long_range_B_refined	2.968
r_long_range_B_other	2.85
r_angle_refined_deg	2.256
r_mcangle_it	1.719
r_mcangle_other	1.719
r_angle_other_deg	1.582
r_mcbond_it	1.551
r_mcbond_other	1.549
r_chiral_restr	0.139
r_bond_refined_d	0.02
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5568
Nucleic Acid Atoms
Solvent Atoms	673
Heterogen Atoms	126

Software

Software
Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
d*TREK	data reduction
O	model building