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Shikimate 5-Dehydrogenase (aroE) from Helicobacter pylori in complex with Shikimate and NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PHG PDB ENTRY 3PHG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 25% PEG 8000, 0.1M BIS-TRIS, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 44.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.99 α = 90 b = 48.391 β = 97.61 c = 123.002 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 110 CCD ADSC QUANTUM 210 2008-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 0.9762 NSRRC BL13C1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.04 30 96.9 0.037 0.037 32.2 4.4 32329 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.12 90.9 0.131 0.131 10.3 4.2 2979
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 3PHG 2.04 28.23 32345 30682 1646 96.17 0.20896 0.20774 0.2063 0.23124 0.2299 RANDOM 34.245
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] 4.15 -0.91 -2.18 -2.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.637 r_dihedral_angle_4_deg 18.736 r_dihedral_angle_3_deg 16.001 r_scangle_it 7.306 r_dihedral_angle_1_deg 5.945 r_scbond_it 4.975 r_mcangle_it 3.156 r_mcbond_it 1.931 r_angle_refined_deg 1.656 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.637 r_dihedral_angle_4_deg 18.736 r_dihedral_angle_3_deg 16.001 r_scangle_it 7.306 r_dihedral_angle_1_deg 5.945 r_scbond_it 4.975 r_mcangle_it 3.156 r_mcbond_it 1.931 r_angle_refined_deg 1.656 r_chiral_restr 0.112 r_gen_planes_refined 0.018 r_bond_refined_d 0.015 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 4054 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 120
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling