1XM8

X-RAY STRUCTURE OF GLYOXALASE II FROM ARABIDOPSIS THALIANA GENE AT2G31350


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.529310 MG/ML PROTEIN, 0.100 SODIUM ACETATE, 16 PERCENT PEG 4K, 10 PERCENT PEG 400, 0.200 GLYCINE, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 4.50
Crystal Properties
Matthews coefficientSolvent content
2.3247.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.494α = 90
b = 58.782β = 109.22
c = 69.049γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4BENT CYLINDRICAL SI- MIRROR (RH COATING)2004-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-DAPS14-BM-D

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
11.74233.7297.40.07921.27.651949
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)
1.741.892.90.5454.347.3

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 DIFFRACTIONSADTHROUGHOUT1.7433.7149295263097.70.1420.140.189RANDOM14.89
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]
0.4420.0120.206-0.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.794
r_dihedral_angle_4_deg18.904
r_dihedral_angle_3_deg14.118
r_scangle_it6.477
r_dihedral_angle_1_deg6.249
r_scbond_it4.976
r_sphericity_bonded2.927
r_mcangle_it2.633
r_mcbond_it2.284
r_sphericity_free2.033
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.794
r_dihedral_angle_4_deg18.904
r_dihedral_angle_3_deg14.118
r_scangle_it6.477
r_dihedral_angle_1_deg6.249
r_scbond_it4.976
r_sphericity_bonded2.927
r_mcangle_it2.633
r_mcbond_it2.284
r_sphericity_free2.033
r_angle_refined_deg1.746
r_angle_other_deg0.884
r_mcbond_other0.379
r_symmetry_vdw_refined0.28
r_symmetry_hbond_refined0.237
r_nbd_refined0.229
r_symmetry_vdw_other0.209
r_nbd_other0.185
r_xyhbond_nbd_refined0.184
r_nbtor_refined0.179
r_metal_ion_refined0.116
r_chiral_restr0.107
r_nbtor_other0.087
r_bond_refined_d0.02
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_rigid_bond_restr
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4027
Nucleic Acid Atoms
Solvent Atoms562
Heterogen Atoms4

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
ARP/wARPmodel building
RESOLVEphasing
REFMACrefinement