4NG5 | pdb_00004ng5

V203A horse liver alcohol dehydrogenase E 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	4DWV	PDB ENTRY 4DWV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICRODIALYSIS	7	278	50 mM ammonium N-[tris(hydrozymethyl)methyl]-2-aminoethanesulfonate and 0.5 mM EDTA, pH 6.7 (at 25 deg C), 10 mg/ml protein, 1 mM NAD+, 10 mM 2,3,4,5,6-pentafluorobenzyl alcohol, 13-25 % 2-methyl-2,4-pentanediol, MICRODIALYSIS, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.52	α = 91.8
b = 51.56	β = 103.05
c = 92.55	γ = 110.3

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	MARMOSAIC 300 mm CCD	ADJUSTABLE FOCUS K-B PAIR SI PLUS PT, RH COATINGS DOUBLE CRYSTAL CRYOCOOLED SI(111)	2007-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.0332	APS	23-ID-D

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	1.1	20	86.2	0.068	15.5	5.25	261399				10.5

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	1.1	1.14	54.2		0.249	3.8	3.44	16455

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1.1	17.91	261399	258723	2681	86.19	0.11985	0.11985	0.11968	0.12	0.13655	0.14	RANDOM	17.529

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]
0.3	-0.63	0.28	0.42	0.04	-0.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.129
r_sphericity_free	36.622
r_dihedral_angle_4_deg	11.957
r_dihedral_angle_3_deg	11.093
r_sphericity_bonded	9.164
r_dihedral_angle_1_deg	6.29
r_long_range_B_refined	3.713
r_rigid_bond_restr	3.337
r_long_range_B_other	2.796
r_scangle_other	2.343
r_scbond_other	2.035
r_scbond_it	2.033
r_angle_refined_deg	1.792
r_mcangle_it	1.289
r_mcangle_other	1.289
r_mcbond_it	1.067
r_mcbond_other	1.066
r_angle_other_deg	0.885
r_chiral_restr	0.105
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
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	1052
Heterogen Atoms	150

Software

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