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Crystal Structure of YagE, a KDG aldolase protein in complex with Magnesium cation coordinated L-glyceraldehyde
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Microbatch under oil 6.5 298 15%PEG 3350, 100mM Hepes pH 6.5, 200mM MgCl2, Microbatch under oil, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.05 39.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.2 α = 90 b = 155.07 β = 90 c = 55.4 γ = 90
Symmetry Space Group P 21 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 2012-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.976 ESRF BM14
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 1.99 48.94 99 0.1 18.14 83868 -3
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 1.99 2.04 89.4 0.531 4.13
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.99 48.94 79674 4194 99.03 0.17583 0.17438 0.1852 0.20332 0.216 RANDOM 16.539
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] -1.2 1.3 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.926 r_dihedral_angle_4_deg 20.864 r_dihedral_angle_3_deg 12.083 r_dihedral_angle_1_deg 6.16 r_scbond_it 2.252 r_mcangle_it 1.852 r_angle_refined_deg 1.761 r_angle_other_deg 1.348 r_mcbond_it 1.347 r_mcbond_other 1.346
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.926 r_dihedral_angle_4_deg 20.864 r_dihedral_angle_3_deg 12.083 r_dihedral_angle_1_deg 6.16 r_scbond_it 2.252 r_mcangle_it 1.852 r_angle_refined_deg 1.761 r_angle_other_deg 1.348 r_mcbond_it 1.347 r_mcbond_other 1.346 r_chiral_restr 0.114 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_bond_other_d 0.009 r_gen_planes_other 0.006 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined 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 9043 Nucleic Acid Atoms Solvent Atoms 525 Heterogen Atoms 90
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction