3ZI1

Crystal structure of human glyoxalase domain-containing protein 4 (GLOD4)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FA8PDB ENTRY 1FA8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.2M MAGNESIUM CHLORIDE, 0.1M HEPES PH 7.5, 25%(W/V) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3748.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.291α = 90
b = 42.918β = 90
c = 68.103γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.8968.198.20.18.94.4279352.220.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.89297.40.532.24.5

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1FA81.9119.2926497141997.690.167130.165110.160.203980.2RANDOM23.639
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]
-0.07-0.090.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.84
r_dihedral_angle_4_deg19.798
r_dihedral_angle_3_deg12.278
r_dihedral_angle_1_deg5.63
r_angle_refined_deg1.463
r_chiral_restr0.104
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2151
Nucleic Acid Atoms
Solvent Atoms367
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing