9U4X | pdb_00009u4x

Crystal Structure of Alcohol Dehydrogenase from Anoxybacillus geothermalis D9

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	0.2M Magnesium chloride hexahydrate, 0.1M Bis Tris 5.5, 25% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.607	α = 90
b = 130.769	β = 90.704
c = 134.918	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	293.15	PIXEL	DECTRIS EIGER X 16M		2024-02-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.7	48.97	99.81	0.082	0.983	7.9	2		79921

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.7	48.97	79628	4047	99.911	0.202	0.2003	0.2003	0.2408	0.2407	45.69

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]
0.064		-0.053	0.014		-0.077

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.547
r_dihedral_angle_6_deg	15.321
r_lrange_other	14.588
r_lrange_it	14.587
r_scangle_it	11.866
r_scangle_other	11.865
r_dihedral_angle_2_deg	11.66
r_mcangle_it	9.005
r_mcangle_other	9.005
r_scbond_it	8.075
r_scbond_other	8.075
r_dihedral_angle_1_deg	7.71
r_mcbond_it	6.054
r_mcbond_other	6.049
r_angle_refined_deg	2.433
r_angle_other_deg	0.842
r_metal_ion_refined	0.583
r_xyhbond_nbd_refined	0.271
r_symmetry_nbd_refined	0.247
r_nbd_other	0.231
r_nbd_refined	0.216
r_symmetry_xyhbond_nbd_other	0.201
r_symmetry_nbd_other	0.163
r_nbtor_refined	0.16
r_chiral_restr	0.115
r_symmetry_xyhbond_nbd_refined	0.113
r_symmetry_nbtor_other	0.078
r_ncsr_local_group_7	0.059
r_ncsr_local_group_18	0.058
r_ncsr_local_group_5	0.056
r_ncsr_local_group_27	0.056
r_ncsr_local_group_16	0.055
r_ncsr_local_group_2	0.054
r_ncsr_local_group_3	0.054
r_ncsr_local_group_13	0.054
r_ncsr_local_group_23	0.054
r_ncsr_local_group_1	0.053
r_ncsr_local_group_4	0.053
r_ncsr_local_group_10	0.053
r_ncsr_local_group_6	0.051
r_ncsr_local_group_17	0.051
r_ncsr_local_group_22	0.051
r_ncsr_local_group_26	0.051
r_ncsr_local_group_15	0.05
r_ncsr_local_group_8	0.049
r_ncsr_local_group_11	0.049
r_ncsr_local_group_12	0.048
r_ncsr_local_group_14	0.048
r_ncsr_local_group_9	0.047
r_ncsr_local_group_19	0.047
r_ncsr_local_group_21	0.046
r_ncsr_local_group_28	0.046
r_ncsr_local_group_20	0.045
r_ncsr_local_group_25	0.044
r_ncsr_local_group_24	0.041
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20256
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms	16

Software

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