7WT1

human glyoxalase I (with C-ter His tag) in inhibitor-free form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3VW9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M NaCl, 0.1 M MES-NaOH, 25% PEG3350
Crystal Properties
Matthews coefficientSolvent content
1.9135.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.53α = 90
b = 65.221β = 102.3
c = 41.382γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95PIXELDECTRIS EIGER X 16M2020-10-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.98000Photon FactoryBL-17A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.852099.20.0630.99910.93.52807927.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.9599.50.70.7791.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT3vw91.8519.7225229283599.150.19640.19270.2296RANDOM37.769
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]
0.060.01-0.080.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.609
r_dihedral_angle_3_deg13.715
r_dihedral_angle_4_deg10.607
r_dihedral_angle_1_deg7.34
r_angle_refined_deg1.454
r_angle_other_deg1.331
r_chiral_restr0.081
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.609
r_dihedral_angle_3_deg13.715
r_dihedral_angle_4_deg10.607
r_dihedral_angle_1_deg7.34
r_angle_refined_deg1.454
r_angle_other_deg1.331
r_chiral_restr0.081
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2800
Nucleic Acid Atoms
Solvent Atoms97
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing