8QNB | pdb_00008qnb

Crystal structure of ancestral L-galactono-1,4-lactone dehydrogenase: in complex with L-galactono-1,4-lactone

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	20% PEG3350, 0.2 M Lithium Nitrate

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.527	α = 90
b = 69.964	β = 103.72
c = 71.239	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 EIGER R 4M		2023-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.9677	ESRF	ID30B

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	2.1	49.25	98.4	0.096	0.101	0.031	0.999	13.9	10.6		31671

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	2.1	2.16		99	1.891	1.992	0.62	0.787		10.1

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	2.1	49.25	30085	1570	98.3	0.20225	0.19959	0.21	0.25433	0.27	RANDOM	46.393

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]
3.45		-5.64	0.57		-1.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.578
r_dihedral_angle_4_deg	17.519
r_dihedral_angle_3_deg	15.271
r_long_range_B_refined	7.783
r_long_range_B_other	7.782
r_dihedral_angle_1_deg	7.134
r_scangle_other	5.911
r_mcangle_it	4.916
r_mcangle_other	4.915
r_scbond_it	3.877
r_scbond_other	3.876
r_mcbond_it	3.321
r_mcbond_other	3.321
r_angle_refined_deg	1.49
r_angle_other_deg	1.245
r_chiral_restr	0.19
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
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	3754
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms	65

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling