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Crystal structure of glyoxalase III (Orf 19.251) from Candida albicans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RW7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.1 277 100 mM sodium acetate pH 4.1, 120 mM ammonium acetate, 27% PEG4000 and 3% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.42 49.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.23 α = 90 b = 92.23 β = 90 c = 59.367 γ = 90
Symmetry Space Group P 42 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 325 mm CCD 2011-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 41 100 0.05 51.1 12.1 34390 21
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 100 1 2.2 12.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1RW7 1.6 41 34216 32486 1730 99.6 0.159 0.158 0.1689 0.185 0.1946 RANDOM 25.58
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] 0.44 0.44 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.986 r_dihedral_angle_4_deg 15.712 r_dihedral_angle_3_deg 13.214 r_dihedral_angle_1_deg 9.034 r_long_range_B_refined 6.347 r_long_range_B_other 6.346 r_scangle_other 3.377 r_scbond_other 2.363 r_scbond_it 2.361 r_mcangle_other 2.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.986 r_dihedral_angle_4_deg 15.712 r_dihedral_angle_3_deg 13.214 r_dihedral_angle_1_deg 9.034 r_long_range_B_refined 6.347 r_long_range_B_other 6.346 r_scangle_other 3.377 r_scbond_other 2.363 r_scbond_it 2.361 r_mcangle_other 2.008 r_mcangle_it 2.004 r_mcbond_it 1.503 r_mcbond_other 1.478 r_angle_refined_deg 1.081 r_angle_other_deg 0.63 r_chiral_restr 0.077 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_gen_planes_other 0.001 r_bond_other_d 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 Atoms Number Protein Atoms 1843 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 8
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling