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Engineering the enolase active site pocket: Crystal structure of the S39N D321A mutant of yeast enolase 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XH0 PDB ENTRY 2XH0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 18 % PEG 3350, 0.2 M POTASSIUM SULFATE
Crystal Properties Matthews coefficient Solvent content 2.51 51.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.72 α = 89.41 b = 82.54 β = 71.31 c = 95.61 γ = 84.8
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 2008-10-08 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 1.79 40 93.1 0.13 12.74 2.01 162601 2 25.2
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 1.79 1.9 87.3 0.49 3.48 1.77
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 2XH0 1.8 35.65 154614 8146 93.5 0.16797 0.16579 0.1658 0.20949 0.2077 RANDOM 18.841
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 37.996 r_dihedral_angle_4_deg 13.888 r_dihedral_angle_3_deg 12.826 r_dihedral_angle_1_deg 5.644 r_scangle_it 2.513 r_scbond_it 1.631 r_angle_refined_deg 1.181 r_mcangle_it 0.971 r_mcbond_it 0.612 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.996 r_dihedral_angle_4_deg 13.888 r_dihedral_angle_3_deg 12.826 r_dihedral_angle_1_deg 5.644 r_scangle_it 2.513 r_scbond_it 1.631 r_angle_refined_deg 1.181 r_mcangle_it 0.971 r_mcbond_it 0.612 r_nbtor_refined 0.299 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.176 r_symmetry_hbond_refined 0.137 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.082 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 13104 Nucleic Acid Atoms Solvent Atoms 2567 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing