6C7L | pdb_00006c7l

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6C76

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	298	0.4 M NH4H2PO4, pH 4.2

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.304	α = 90
b = 69.304	β = 90
c = 166.644	γ = 90

Symmetry
Space Group	P 43 21 2

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	RIGAKU SATURN 944+	osmic mirrors	2014-10-20	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	1.909	29	95.2	0.096	0.098	0.02	0.999	12.5	20.7		30956			28.8

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	1.909	1.93	84.6		0.673	0.768	0.355	0.647	1.6	3.9

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	6C76	1.91	29	28792	1997	94.83	0.14011	0.13668	0.15	0.18939	0.2	RANDOM	42.895

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]
0.13			0.13		-0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.225
r_dihedral_angle_4_deg	19.779
r_dihedral_angle_3_deg	16.118
r_long_range_B_refined	9.389
r_long_range_B_other	9.388
r_dihedral_angle_1_deg	6.258
r_scangle_it	5.235
r_scangle_other	5.234
r_scbond_it	3.425
r_scbond_other	3.424
r_mcangle_other	3.034
r_mcangle_it	3.033
r_mcbond_it	2.222
r_mcbond_other	2.22
r_angle_refined_deg	1.122
r_angle_other_deg	0.679
r_symmetry_vdw_refined	0.278
r_nbd_refined	0.247
r_nbtor_refined	0.185
r_symmetry_vdw_other	0.174
r_nbd_other	0.172
r_symmetry_hbond_refined	0.14
r_xyhbond_nbd_refined	0.119
r_nbtor_other	0.084
r_chiral_restr	0.075
r_xyhbond_nbd_other	0.045
r_gen_planes_refined	0.012
r_bond_refined_d	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001
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	2926
Nucleic Acid Atoms
Solvent Atoms	462
Heterogen Atoms	138

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing