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Crystal structure of V278E-glyoxalase I mutant from Zea mays in space group P6(3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D7Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.7 294 sodium formate 4.2 M pH 9.7, 0.5% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.25 45.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.11 α = 90 b = 82.11 β = 90 c = 74.97 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M Kirkpatrick-Baez pair of bi-morph mirrors 2016-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9801 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 1.8 41.06 99.9 0.067 1 19.7 10.27 26692
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.91 99.5 1.375 0.666 1.4 10.32
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5D7Z 1.8 41.05 25355 1335 99.9 0.1855 0.18346 0.1814 0.22406 0.2215 RANDOM 38.629
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] 0.72 0.36 0.72 -2.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.188 r_dihedral_angle_4_deg 17.972 r_dihedral_angle_3_deg 15.064 r_long_range_B_refined 7.446 r_dihedral_angle_1_deg 6.998 r_mcangle_it 4.341 r_scbond_it 4.033 r_mcbond_it 3.034 r_angle_refined_deg 1.624 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.188 r_dihedral_angle_4_deg 17.972 r_dihedral_angle_3_deg 15.064 r_long_range_B_refined 7.446 r_dihedral_angle_1_deg 6.998 r_mcangle_it 4.341 r_scbond_it 4.033 r_mcbond_it 3.034 r_angle_refined_deg 1.624 r_chiral_restr 0.122 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2222 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing