8HAP | pdb_00008hap

Crystal structure of thermostable acetaldehyde dehydrogenase from hyperthermophilic archaeon Sulfolobus tokodaii

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3PQA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	293	100 mM sodium phosphate dibasic/citric acid (pH 4.2), 200 mM sodium chloride, 10% (v/v) polyethylene glycol (PEG) 3000

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 164.075	α = 90
b = 75.356	β = 124.64
c = 105.305	γ = 90

Symmetry
Space Group	C 1 2 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	PIXEL	DECTRIS EIGER X 16M		2018-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	1.0000	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.197	86.635	99	0.087	0.104	0.056	9.9	3.4	53563	53563

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.32	97.7		0.588	0.588	0.704	0.383	1.3	3.3

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	3PQA	2.2	46.6	50864	2699	98.99	0.1702	0.168	0.1743	0.2136	0.2147	RANDOM	36.577

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]
		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.738
r_dihedral_angle_4_deg	20.502
r_dihedral_angle_3_deg	16.709
r_dihedral_angle_1_deg	7.086
r_angle_refined_deg	1.56
r_angle_other_deg	1.289
r_chiral_restr	0.071
r_bond_refined_d	0.009
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	7176
Nucleic Acid Atoms
Solvent Atoms	267
Heterogen Atoms	72

Software

Software
Software Name	Purpose
XDS	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction