3OQ6 | pdb_00003oq6

Horse liver alcohol dehydrogenase A317C mutant complexed with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HLD	PDB entry 1hld

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICRODIALYSIS	7	298	50 mM ammonium TES [N-tris(hydroxymethyl)-2-aminoethane sulfonate], 25% MRD, 11 mg/ml protein, 11 mM NAD+, 5 mM 2,3,4,5,6-pentafluorobenzyl alcohol, pH 7.0, MICRODIALYSIS, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.34	α = 91.98
b = 51.31	β = 102.95
c = 92.21	γ = 110.11

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	NOIR-1	SAGGITALLY FOCUSED MIRRORS	2009-03-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	0.80	ALS	4.2.2

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	1.2	90	92.2	0.061	9.4	3.57		214213			11.5

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	1.2	1.24	83.6		0.281	3	3.43	19347

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	PDB entry 1hld	1.2	19.85	214172	1061	92.29	0.1351	0.135	0.14	0.1621	0.17	RANDOM	17.5778

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	-0.31	0.41	-0.32	0.12	0.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.981
r_dihedral_angle_4_deg	12.894
r_dihedral_angle_3_deg	11.074
r_dihedral_angle_1_deg	6.182
r_scangle_it	4.959
r_scbond_it	3.343
r_mcangle_it	2.344
r_angle_refined_deg	1.616
r_mcbond_it	1.581
r_rigid_bond_restr	1.331

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.981
r_dihedral_angle_4_deg	12.894
r_dihedral_angle_3_deg	11.074
r_dihedral_angle_1_deg	6.182
r_scangle_it	4.959
r_scbond_it	3.343
r_mcangle_it	2.344
r_angle_refined_deg	1.616
r_mcbond_it	1.581
r_rigid_bond_restr	1.331
r_angle_other_deg	0.989
r_mcbond_other	0.84
r_chiral_restr	0.096
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5572
Nucleic Acid Atoms
Solvent Atoms	1098
Heterogen Atoms	142

Software

Software
Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
d*TREK	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.