8G39 | pdb_00008g39

Horse liver alcohol dehydrogense His-51-Gln form complexed with NADH and N-cyclohexylformamide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QV6	F51Q/K228R ADH complexed with NAD+ and 2,4-difluorobenzyl alcohol

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, 1 mM NADH and 15 mM N-cyclohexylformamide, 13 % 2-methyl-2,4-pentanediol,raised to 25% MPD before crystal pliunged into liquid N2.

Crystal Properties
Matthews coefficient	Solvent content
2.25	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.08	α = 92.1
b = 50.92	β = 102.95
c = 92.74	γ = 109.68

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	2004-02-04	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	19.9	87.9	0.028	0.036	16	2.35		121863

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		71.2	0.248	0.324		2.35

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	1qv6	1.42	19.91	119503	2403	87.88	0.14644	0.14554	0.15	0.19063	0.16	RANDOM	21.28

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]
0.47	-0.49	0.09	0.26	0.27	-0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.368
r_dihedral_angle_3_deg	12.526
r_dihedral_angle_4_deg	11.214
r_dihedral_angle_1_deg	6.712
r_rigid_bond_restr	4.258
r_scangle_other	3.849
r_long_range_B_refined	3.802
r_scbond_it	3.769
r_scbond_other	3.769
r_long_range_B_other	3.675
r_mcangle_it	2.641
r_mcangle_other	2.64
r_mcbond_it	2.386
r_mcbond_other	2.386
r_angle_refined_deg	2.079
r_angle_other_deg	1.555
r_chiral_restr	0.114
r_bond_refined_d	0.017
r_gen_planes_refined	0.012
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	640
Heterogen Atoms	118

Software

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