4NFH | pdb_00004nfh

V207A Horse Liver Alcohol Dehydrogenase E 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	PDB ENTRY 4DWV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICRODIALYSIS	7	278	50 mM ammonium n-[tris(hydroxymethyl) methyl]-2-aminoethane sulfonate, pH 6.7 (at 25 C), 0.25 mM EDTA, 10 mg/ml protein, 1 mM NAD+, 10 mM 2,3,4,5,6-pentafluorobenzyl alcohol, 12 TO 25 % 2-methyl-2,4-pentanediol, MICRODIALYSIS, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.49	α = 91.96
b = 51.23	β = 103
c = 92.32	γ = 110.28

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	Rosenbaum vertical focussing mirrors	2008-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	0.827	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	20	94.2	0.055	11.3	3.77		217807			11.9

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	74		0.363	2.4	3.46	17131

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 (All)	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 4DWV	1.2	19.84	216747	1066	94.14	0.13547	0.13547	0.13532	0.14	0.16569	0.17	RANDOM	16.966

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]
0.24	-0.49	0.24	0.23	0.15	-0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	41.554
r_dihedral_angle_2_deg	38.114
r_dihedral_angle_4_deg	14.701
r_dihedral_angle_3_deg	11.387
r_sphericity_bonded	10.42
r_dihedral_angle_1_deg	6.244
r_long_range_B_refined	5.096
r_rigid_bond_restr	3.921
r_long_range_B_other	3.814
r_scangle_other	3.088
r_scbond_it	2.764
r_scbond_other	2.764
r_angle_refined_deg	1.892
r_mcangle_it	1.653
r_mcangle_other	1.653
r_mcbond_it	1.443
r_mcbond_other	1.443
r_angle_other_deg	0.911
r_chiral_restr	0.11
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5566
Nucleic Acid Atoms
Solvent Atoms	994
Heterogen Atoms	150

Software

Software
Software Name	Purpose
Blu-Ice	data collection
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling