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Crystal structure of enolase brado_4202 (target EFI-501651) from Bradyrhizobium complexed with magnesium and mandelic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TOY PDB ENTRY 3TOY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 0.3M MAGNESIUM FORMATE, 100MM BIS-TRIS, PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.59 52.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.949 α = 90 b = 118.867 β = 90 c = 130.571 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 MIRRORS 2011-07-23 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 50 99.9 0.088 7.9 7.4 57954 -5 37.757
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 2.03 100 0.95 1 7.3
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 3TOY 2 50 56002 1783 99.72 0.20577 0.20392 0.2045 0.26348 0.2586 RANDOM 51.849
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] -0.33 1.14 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.253 r_dihedral_angle_4_deg 18.368 r_dihedral_angle_3_deg 14.912 r_scangle_it 13.028 r_scbond_it 10.655 r_mcangle_it 7.648 r_mcbond_it 5.744 r_dihedral_angle_1_deg 5.312 r_angle_refined_deg 1.246 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.253 r_dihedral_angle_4_deg 18.368 r_dihedral_angle_3_deg 14.912 r_scangle_it 13.028 r_scbond_it 10.655 r_mcangle_it 7.648 r_mcbond_it 5.744 r_dihedral_angle_1_deg 5.312 r_angle_refined_deg 1.246 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 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 5377 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 34
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling