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Probing the active site of the sugar isomerase domain from E. coli arabinose-5-phosphate isomerase via X-ray crystallography
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ETN PDB ENTRY 3ETN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 20% PEG-8000 100MM HEPES PH 7.5 (WIZARD I SCREEN,[EMERALD BIOSYSTEMS] CONDITION 21).
Crystal Properties Matthews coefficient Solvent content 1.8 32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.86 α = 90 b = 67.43 β = 106.94 c = 82.17 γ = 90
Symmetry Space Group P 1 21 1
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 315r 2009-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.6 40 94.3 0.12 5.9 2.7 17026 2 42.7
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 2.6 2.74 95.5 0.36 2.4 2.7
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 3ETN 2.6 40 16148 863 93.68 0.26302 0.26075 0.2619 0.30503 0.3102 RANDOM 36.384
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] 5.16 5.24 -2.76 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.861 r_dihedral_angle_4_deg 15.507 r_dihedral_angle_3_deg 11.61 r_dihedral_angle_1_deg 2.813 r_scangle_it 1.362 r_mcangle_it 0.82 r_scbond_it 0.711 r_mcbond_it 0.443 r_angle_refined_deg 0.43 r_chiral_restr 0.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.861 r_dihedral_angle_4_deg 15.507 r_dihedral_angle_3_deg 11.61 r_dihedral_angle_1_deg 2.813 r_scangle_it 1.362 r_mcangle_it 0.82 r_scbond_it 0.711 r_mcbond_it 0.443 r_angle_refined_deg 0.43 r_chiral_restr 0.031 r_bond_refined_d 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_refined 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_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 5086 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing