8PA1 | pdb_00008pa1

Crystal structure of alcohol dehydrogenase/ketoreductase variant from Thermus thermophilus apo form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2D1Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.8	293	20 % PEG3350, 0.1 M ammonium sulfate, 0.1 M bis-tris propane pH 7.8

Crystal Properties
Matthews coefficient	Solvent content
2.4	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.538	α = 90
b = 95.455	β = 108.06
c = 79.016	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	PIXEL	DECTRIS PILATUS 6M		2021-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.965	ESRF	MASSIF-1

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	2.6	47.8	99.8	0.15	0.182	0.101	0.966	4.7	3.1		31116

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	2.6	2.72		100	0.836	1.012	0.563	0.449		3.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.6	47.8	29547	1540	99.68	0.17998	0.17687	0.19	0.24143	0.25	RANDOM	47.874

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]
-3.64		0.7	2.33		0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.891
r_dihedral_angle_4_deg	21.175
r_dihedral_angle_3_deg	16.274
r_long_range_B_other	10.086
r_long_range_B_refined	10.082
r_scangle_other	7.84
r_dihedral_angle_1_deg	6.931
r_mcangle_it	6.439
r_mcangle_other	6.439
r_scbond_it	5.318
r_scbond_other	5.318
r_mcbond_it	4.322
r_mcbond_other	4.322
r_angle_refined_deg	1.503
r_angle_other_deg	1.251
r_chiral_restr	0.066
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7424
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms	44

Software

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