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Crystal structure of Escherichia coli phosphoheptose isomerase in complex with reaction substrate sedoheptulose 7-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TK9 PDB entry 1TK9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 298 3% PEG 8000, 0.002 M DTT, 3% 1,6-hexanediol, 0.01 M Hepes, 0.1 M imidazole, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.29 46.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.045 α = 90 b = 76.54 β = 106.13 c = 78.316 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 IMAGE PLATE RIGAKU RAXIS IV 2005-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.79 47.39 98.6 20533 20533 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.79 2.89 99.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1TK9 2.8 25 18807 18807 1478 100 0.20694 0.20297 0.1924 0.25699 0.2437 RANDOM 44.337
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] 0.21 -0.51 -0.34 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.003 r_dihedral_angle_4_deg 24.483 r_dihedral_angle_3_deg 20.234 r_dihedral_angle_1_deg 6.752 r_scangle_it 5.438 r_scbond_it 3.83 r_mcangle_it 2.853 r_angle_refined_deg 2.845 r_mcbond_it 2.039 r_nbtor_refined 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.003 r_dihedral_angle_4_deg 24.483 r_dihedral_angle_3_deg 20.234 r_dihedral_angle_1_deg 6.752 r_scangle_it 5.438 r_scbond_it 3.83 r_mcangle_it 2.853 r_angle_refined_deg 2.845 r_mcbond_it 2.039 r_nbtor_refined 0.35 r_nbd_refined 0.301 r_symmetry_vdw_refined 0.243 r_xyhbond_nbd_refined 0.221 r_chiral_restr 0.187 r_symmetry_hbond_refined 0.178 r_bond_refined_d 0.038 r_gen_planes_refined 0.011 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5436 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection CrystalClear data reduction CrystalClear data scaling CNS phasing