8QNC

Crystal structure of ancestral L-galactono-1,4-lactone dehydrogenase: A113G variant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.1520% PEG 3350, 0.2 M Lithium Nitrate
Crystal Properties
Matthews coefficientSolvent content
2.1743.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.387α = 90
b = 69.657β = 98.29
c = 67.608γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER R 4M2023-03-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.9677ESRFID30B

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.766.998.90.0920.1020.0430.99810.75.553389
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)RedundancyNumber Unique Reflections (All)
11.71.7399.41.3361.4770.6180.5935.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.766.950741262398.840.180360.178740.21192RANDOM25.772
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]
-0.12-1.310.240.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.748
r_dihedral_angle_4_deg16.474
r_dihedral_angle_3_deg13.819
r_long_range_B_refined6.961
r_long_range_B_other6.941
r_dihedral_angle_1_deg6.922
r_scangle_other5.447
r_mcangle_it3.689
r_mcangle_other3.688
r_scbond_it3.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.748
r_dihedral_angle_4_deg16.474
r_dihedral_angle_3_deg13.819
r_long_range_B_refined6.961
r_long_range_B_other6.941
r_dihedral_angle_1_deg6.922
r_scangle_other5.447
r_mcangle_it3.689
r_mcangle_other3.688
r_scbond_it3.56
r_scbond_other3.56
r_mcbond_other2.499
r_mcbond_it2.498
r_angle_refined_deg1.678
r_angle_other_deg1.401
r_chiral_restr0.083
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms3823
Nucleic Acid Atoms
Solvent Atoms295
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling