6C75 | pdb_00006c75

Structure of Iron containing alcohol dehydrogenase from Thermococcus thioreducens in a monoclinic crystal form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O2D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	298	0.1 M Sodium acetate, 8% PEG 4000, pH 4.5

Crystal Properties
Matthews coefficient	Solvent content
2.32	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.125	α = 90
b = 99.248	β = 103.16
c = 67.487	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	298	CCD	RIGAKU SATURN 944+	Osmic mirrors	2013-04-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54187

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.4	49.61	79	0.234	0.253	0.092	0.982	12	6.5		23385			48.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49	22		0.749	0.993	0.646	0.368	1.8	1.7

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	1O2D	2.4	49.61	22218	1150	78.88	0.14636	0.14311	0.15	0.2081	0.21	RANDOM	66.1

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]
1.6		2.47	-0.5		-2.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.97
r_dihedral_angle_4_deg	20.353
r_dihedral_angle_3_deg	18.673
r_long_range_B_other	9.807
r_long_range_B_refined	9.804
r_dihedral_angle_1_deg	7.983
r_scangle_it	7.514
r_scangle_other	7.508
r_mcangle_it	5.413
r_mcangle_other	5.412
r_scbond_it	4.706
r_scbond_other	4.701
r_mcbond_it	3.603
r_mcbond_other	3.603
r_angle_refined_deg	0.615
r_angle_other_deg	0.496
r_symmetry_vdw_refined	0.266
r_symmetry_vdw_other	0.231
r_nbd_refined	0.221
r_nbd_other	0.208
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.141
r_nbtor_other	0.093
r_symmetry_hbond_refined	0.085
r_chiral_restr	0.04
r_xyhbond_nbd_other	0.034
r_gen_planes_refined	0.012
r_bond_refined_d	0.003
r_gen_planes_other	0.002
r_bond_other_d
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5852
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	80

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing