9KNP | pdb_00009knp

X-ray structure of Pyrococcus horikoshii OT3 alcohol dehydrogenase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		An initial model was generated by PHYRE2 Server

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	200 mM potassium phosphate, 29% w/v polyethylene glycol 3350, 3 mM NAD+, 10 mM NiCl2, 2% v/v butanol, pH 4.9

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.89	α = 90
b = 75.58	β = 90
c = 166.5	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS		2017-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.94	19.5	98.2	0.99	20.3	6.8		63980

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.94	1.99			0.92

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	An initial model was generated by PHYRE2 Server	1.94	19.497	63980	3170	98.192	0.22	0.2184	0.2258	0.2526	0.2581	21.441

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]
-0.23			-0.114		0.344

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.633
r_dihedral_angle_4_deg	21.004
r_dihedral_angle_3_deg	15.181
r_dihedral_angle_1_deg	7.168
r_lrange_it	5.395
r_lrange_other	5.26
r_scangle_it	3.593
r_scangle_other	3.592
r_scbond_it	2.742
r_scbond_other	2.741
r_mcangle_other	2.243
r_mcangle_it	2.242
r_mcbond_it	1.49
r_mcbond_other	1.486
r_angle_refined_deg	1.284
r_angle_other_deg	1.253
r_symmetry_nbd_refined	0.268
r_nbd_other	0.213
r_nbd_refined	0.204
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.153
r_xyhbond_nbd_refined	0.094
r_symmetry_xyhbond_nbd_refined	0.08
r_symmetry_nbtor_other	0.07
r_chiral_restr	0.067
r_symmetry_xyhbond_nbd_other	0.059
r_gen_planes_refined	0.016
r_bond_refined_d	0.006
r_gen_planes_other	0.006
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5836
Nucleic Acid Atoms
Solvent Atoms	458
Heterogen Atoms	100

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing