8G2L | pdb_00008g2l

Horse liver alcohol dehydrogense His-51 Gln form complexed with NAD+ and 2,2,2-trifluoroethanol

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1N8K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	7	278	10 mg/ml protein, 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminiomethanesulfonate and 0.25 mM EDTA, 2 mM NAD+, 0.1 mM 2,2,2-trifluoroetanol, 13% MPD, crystals soaked with 25% MPD, and 100 mM trifluoroethanol

Crystal Properties
Matthews coefficient	Solvent content
2.26	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.02	α = 92.08
b = 51.08	β = 103
c = 92.61	γ = 109.44

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	IMAGE PLATE	RIGAKU RAXIS IV++	confocal	2004-05-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	1.42	19.87	87.2	0.058	0.063	17.2	6.16		121088

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	1.42	1.47		51.3	0.373	0.417		4.78

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.42	19.88	118680	2406	87.2	0.1868	0.1863	0.18	0.21122	0.2	RANDOM	21.355

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]
0.04	0.25	0.05	1.35	0.2	-1.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.619
r_dihedral_angle_3_deg	12.487
r_dihedral_angle_4_deg	12.188
r_dihedral_angle_1_deg	6.859
r_long_range_B_refined	4.629
r_long_range_B_other	4.486
r_scangle_other	3.693
r_scbond_it	2.591
r_scbond_other	2.59
r_mcangle_other	2.156
r_mcangle_it	2.155
r_angle_refined_deg	1.951
r_mcbond_it	1.666
r_mcbond_other	1.665
r_angle_other_deg	1.485
r_chiral_restr	0.101
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5568
Nucleic Acid Atoms
Solvent Atoms	667
Heterogen Atoms	128

Software

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