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Crystal structure of enolase PRK14017 (target EFI-500653) from Ralstonia pickettii 12J with magnesium bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RR1 PDB entry 3RR1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 294 0.1M TRIS-HCL, 200MM AMMONIUM ACETATE, 25% PEG3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.22 44.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.339 α = 90 b = 117.339 β = 90 c = 113.685 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 2.3 50 94.8 0.095 7.2 4.3 34611 -5 48.346
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 2.3 2.34 92.8 0.9 1.2 4.1
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 3RR1 2.3 50 31342 1028 94.46 0.20763 0.2058 0.205 0.26258 0.2617 RANDOM 66.691
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] -34.05 -34.05 68.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.214 r_dihedral_angle_3_deg 16.52 r_dihedral_angle_4_deg 14.431 r_scangle_it 12.936 r_scbond_it 9.053 r_mcangle_it 5.957 r_dihedral_angle_1_deg 5.403 r_mcbond_it 3.967 r_angle_refined_deg 1.118 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.214 r_dihedral_angle_3_deg 16.52 r_dihedral_angle_4_deg 14.431 r_scangle_it 12.936 r_scbond_it 9.053 r_mcangle_it 5.957 r_dihedral_angle_1_deg 5.403 r_mcbond_it 3.967 r_angle_refined_deg 1.118 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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 5794 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 4
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling