1VLJ | pdb_00001vlj

Crystal structure of NADH-dependent butanol dehydrogenase A (TM0820) from Thermotoga maritima at 1.78 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O2D	TM0820 has been phased with EPMR program (500 generations, default low and high resolution limits) using a model based on the template 1o2d (TM0920)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	5.7	293	0.2M NaCl, 0.2% PEG-1000, 0.1M Na,K-Phosphate pH 5.7 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2	38.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.691	α = 90
b = 129.699	β = 103.61
c = 55.234	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC		2003-09-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1		ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.78	50	93.95	0.041	21.67	2.85		65785			36.93

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.78	1.84	68.72		0.338	1.94	1.87	4773

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	TM0820 has been phased with EPMR program (500 generations, default low and high resolution limits) using a model based on the template 1o2d (TM0920)	1.78	49.6	62407	3343	93.86	0.14475	0.14224	0.16	0.19265	0.16	RANDOM	35.944

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]
-0.38		1.73	-0.47		1.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.7
r_dihedral_angle_4_deg	15.307
r_dihedral_angle_3_deg	13.591
r_scangle_it	7.306
r_dihedral_angle_1_deg	5.671
r_scbond_it	5.538
r_mcangle_it	2.962
r_mcbond_it	2.249
r_angle_refined_deg	1.562
r_angle_other_deg	1
r_mcbond_other	0.617
r_symmetry_vdw_other	0.265
r_nbd_refined	0.234
r_symmetry_vdw_refined	0.211
r_nbd_other	0.18
r_symmetry_hbond_refined	0.16
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.099
r_nbtor_other	0.087
r_xyhbond_nbd_other	0.061
r_bond_refined_d	0.017
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	6078
Nucleic Acid Atoms
Solvent Atoms	480
Heterogen Atoms	98

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
REFMAC	refinement