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Crystal structure of 0.5M urea unfolded YagE, a KDG aldolase protein in complex with Pyruvate
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 6.5 298 15% PEG3350, 200mM MgCl2, 100mM HEPES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.39 47.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.4 α = 90 b = 155.64 β = 90 c = 55.92 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 MARMOSAIC 225 mm CCD 2012-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.9747 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 3.09 19.88 99.67 0.2197 11.88 10.9 23206 33.36
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 3.09 3.2 99.69 0.6216 5.17 11.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2V8Z 3.09 19.88 22044 1161 99.18 0.21349 0.21182 0.24315 0.2095 RANDOM 24.599
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] -2.67 3.27 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.933 r_dihedral_angle_4_deg 22.063 r_dihedral_angle_3_deg 16.321 r_dihedral_angle_1_deg 5.587 r_long_range_B_refined 3.083 r_long_range_B_other 3.083 r_scangle_other 1.934 r_mcangle_it 1.712 r_mcangle_other 1.712 r_angle_refined_deg 1.341
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.933 r_dihedral_angle_4_deg 22.063 r_dihedral_angle_3_deg 16.321 r_dihedral_angle_1_deg 5.587 r_long_range_B_refined 3.083 r_long_range_B_other 3.083 r_scangle_other 1.934 r_mcangle_it 1.712 r_mcangle_other 1.712 r_angle_refined_deg 1.341 r_scbond_it 1.145 r_scbond_other 1.145 r_mcbond_it 1.029 r_mcbond_other 1.028 r_angle_other_deg 1.006 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.004 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 9039 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement