9W6Y | pdb_00009w6y

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

X-RAY DIFFRACTION

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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) polyethylene glycol 8000 200 mM ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.297	α = 90
b = 90.51	β = 90
c = 96.58	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 EIGER X 16M		2021-08-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

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	1.35	48.3	93.1	0.999	36.8	12.1		141062

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	1.35	1.38			0.942

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	1.5	48.29	111249	5562	99.641	0.168	0.167	0.173	0.1811	0.1858	RANDOM	13.745

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]
0.007			0.217		-0.223

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.885
r_dihedral_angle_3_deg	11.209
r_dihedral_angle_1_deg	5.622
r_dihedral_angle_2_deg	5.562
r_lrange_it	3.578
r_lrange_other	3.405
r_scangle_it	2.396
r_scangle_other	2.396
r_scbond_it	1.645
r_scbond_other	1.644
r_dihedral_angle_other_2_deg	1.584
r_angle_refined_deg	1.444
r_mcangle_it	1.387
r_mcangle_other	1.387
r_mcbond_it	0.971
r_mcbond_other	0.951
r_angle_other_deg	0.842
r_nbd_refined	0.229
r_symmetry_nbd_other	0.205
r_nbd_other	0.179
r_nbtor_refined	0.172
r_symmetry_xyhbond_nbd_refined	0.148
r_symmetry_nbd_refined	0.139
r_xyhbond_nbd_refined	0.112
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.075
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.007
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4980
Nucleic Acid Atoms
Solvent Atoms	653
Heterogen Atoms	120

Software

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