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Engineering the enolase active site pocket: Crystal structure of the S39N Q167K D321R mutant of yeast enolase 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ONE PDB ENTRY 2ONE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 25% PEG 4000, 0.1M SODIUM ACETATE PH 4.6
Crystal Properties Matthews coefficient Solvent content 1.93 36.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.329 α = 89.89 b = 60.797 β = 89.9 c = 120.667 γ = 65.84
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 PILATUS 6M 2008-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 1.7 40 93 0.16 9.69 1.97 147095 2 22.3
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 1.7 1.8 86.9 0.77 2.34 1.67
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 PDB ENTRY 2ONE 1.7 37.85 139807 7411 93.2 0.199 0.197 0.1981 0.246 0.2476 RANDOM 15.41
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.048 r_dihedral_angle_4_deg 16.566 r_dihedral_angle_3_deg 14.106 r_dihedral_angle_1_deg 6.064 r_scangle_it 2.793 r_scbond_it 1.835 r_angle_refined_deg 1.315 r_mcangle_it 1.074 r_mcbond_it 0.691 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.048 r_dihedral_angle_4_deg 16.566 r_dihedral_angle_3_deg 14.106 r_dihedral_angle_1_deg 6.064 r_scangle_it 2.793 r_scbond_it 1.835 r_angle_refined_deg 1.315 r_mcangle_it 1.074 r_mcbond_it 0.691 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.267 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.204 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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_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 13123 Nucleic Acid Atoms Solvent Atoms 1569 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing