9W7A | pdb_00009w7a

Crystal structure of L-galactose dehydrogenase from Luteolibacter sp. strain LG18 in complex with L-glucose and NADP+

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7EZI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	30%(w/v) PEG 8000 200 mM Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.329	α = 90
b = 89.954	β = 90
c = 96.2	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	95	PIXEL	DECTRIS PILATUS3 6M		2021-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A

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	1.56	48.1	100	0.999	21.1	6.1		98431

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	1.56	1.59			0.77

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.56	45.017	98353	4860	99.943	0.161	0.1596	0.1724	0.1838	0.1954	RANDOM	17.931

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]
-0.659			0.438		0.221

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.153
r_dihedral_angle_3_deg	12.427
r_dihedral_angle_2_deg	7.18
r_dihedral_angle_1_deg	5.681
r_lrange_it	4.686
r_lrange_other	4.44
r_scangle_it	3.374
r_scangle_other	3.373
r_scbond_it	2.255
r_scbond_other	2.255
r_mcangle_it	1.686
r_mcangle_other	1.685
r_angle_refined_deg	1.496
r_mcbond_it	1.195
r_mcbond_other	1.194
r_dihedral_angle_other_2_deg	0.673
r_angle_other_deg	0.557
r_symmetry_nbd_refined	0.29
r_nbd_other	0.273
r_nbd_refined	0.234
r_symmetry_nbd_other	0.202
r_symmetry_xyhbond_nbd_refined	0.194
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.076
r_gen_planes_refined	0.008
r_bond_refined_d	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	4971
Nucleic Acid Atoms
Solvent Atoms	801
Heterogen Atoms	120

Software

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