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Engineering the enolase active site pocket: Crystal structure of the S39A D321A mutant of yeast enolase 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XH2 PDB ENTRY 2XH2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 18% PEG 6000, 0.2M MAGNESIUM CHLORIDE
Crystal Properties Matthews coefficient Solvent content 1.89 34.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.421 α = 87.95 b = 62.606 β = 76.07 c = 100.948 γ = 76.43
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 2009-03-25 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 92.4 0.21 8.64 2.01 146644 2 25.7
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 91.1 0.83 2.65 1.93
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 2XH2 1.7 31.69 139761 7363 92.8 0.236 0.233 0.2341 0.279 0.2804 RANDOM 20.46
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 36.213 r_dihedral_angle_4_deg 17.105 r_dihedral_angle_3_deg 13.681 r_dihedral_angle_1_deg 6.274 r_scangle_it 3.583 r_scbond_it 2.428 r_angle_refined_deg 1.603 r_mcangle_it 1.465 r_mcbond_it 0.991 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.213 r_dihedral_angle_4_deg 17.105 r_dihedral_angle_3_deg 13.681 r_dihedral_angle_1_deg 6.274 r_scangle_it 3.583 r_scbond_it 2.428 r_angle_refined_deg 1.603 r_mcangle_it 1.465 r_mcbond_it 0.991 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.266 r_xyhbond_nbd_refined 0.258 r_nbd_refined 0.229 r_symmetry_vdw_refined 0.196 r_chiral_restr 0.104 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 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 12642 Nucleic Acid Atoms Solvent Atoms 1693 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing