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Crystal structure of enolase PRK14017 (target EFI-500653) from Ralstonia pickettii 12J
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GL5 PDB entry 2GL5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 0.1M HEPES, 5% TASCIMATE, 10% PEG5000 MME, 10% GLYCEROL, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.21 44.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.011 α = 90 b = 118.011 β = 90 c = 114.57 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD ADSC QUANTUM 315 MIRRORS 2009-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.95 50 94.7 0.069 10.8 12.2 57169 -5 31.085
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 1.95 1.98 94.7 0.87 2.2 12.4
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 MR THROUGHOUT PDB entry 2GL5 1.95 50 52167 1657 94.23 0.13677 0.1356 0.1354 0.17359 0.1746 RANDOM 44.418
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] -16.41 -16.41 32.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.3 r_dihedral_angle_3_deg 16.277 r_dihedral_angle_4_deg 14.725 r_scangle_it 8.293 r_scbond_it 5.934 r_dihedral_angle_1_deg 5.723 r_mcangle_it 4.993 r_mcbond_it 3.515 r_angle_refined_deg 1.306 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.3 r_dihedral_angle_3_deg 16.277 r_dihedral_angle_4_deg 14.725 r_scangle_it 8.293 r_scbond_it 5.934 r_dihedral_angle_1_deg 5.723 r_mcangle_it 4.993 r_mcbond_it 3.515 r_angle_refined_deg 1.306 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5745 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 11
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling