☰ Navigation Tabs
Crystal structure of YagE, a KDG aldolase protein, in complex with aldol condensed product of pyruvate and glyoxal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V8Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH UNDER OIL 6.5 298 100mM HEPES pH 6.5, 200mM Magnesium chloride, 15% PEG 3350, MICROBATCH UNDER OIL, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.06 40.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.24 α = 90 b = 155.14 β = 90 c = 55.58 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 0.97625 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 8.89 98.2 14.43 4.1 83414
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.04 87 2.76 3.42
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 2V8Z 1.99 49.06 83414 79242 4171 98.27 0.1998 0.19804 0.2066 0.23308 0.239 RANDOM 19.011
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] -1.33 1.1 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.378 r_dihedral_angle_4_deg 21.045 r_dihedral_angle_3_deg 12.478 r_dihedral_angle_1_deg 6.229 r_long_range_B_other 4.106 r_long_range_B_refined 4.105 r_scangle_other 3.191 r_scbond_other 2.19 r_scbond_it 2.161 r_mcangle_it 1.946
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.378 r_dihedral_angle_4_deg 21.045 r_dihedral_angle_3_deg 12.478 r_dihedral_angle_1_deg 6.229 r_long_range_B_other 4.106 r_long_range_B_refined 4.105 r_scangle_other 3.191 r_scbond_other 2.19 r_scbond_it 2.161 r_mcangle_it 1.946 r_mcangle_other 1.943 r_angle_refined_deg 1.896 r_mcbond_it 1.436 r_mcbond_other 1.435 r_angle_other_deg 1.356 r_chiral_restr 0.127 r_bond_refined_d 0.021 r_bond_other_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 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 9037 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 192
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling