☰ Navigation Tabs
Shikimate 5-Dehydrogenase (aroE) from Helicobacter pylori in complex with Shikimate
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 5.5 293 30% PEG 8000, 0.1M BIS-TRIS, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.1 41.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.37 α = 90 b = 62.798 β = 90 c = 84.38 γ = 90
Symmetry Space Group P 21 21 21
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 315r 2008-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0000 NSRRC BL13B1
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 1.42 30 99.8 0.054 0.054 33.8 7 47067 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 1.42 1.47 98.6 0.467 0.467 4.1 6.7 4566
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 1.42 24.85 47133 44685 2382 99.83 0.19884 0.1973 0.196 0.22728 0.225 RANDOM 16.377
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] 0.05 0.48 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.054 r_dihedral_angle_3_deg 10.661 r_dihedral_angle_4_deg 6.751 r_dihedral_angle_1_deg 3.597 r_scangle_it 3.514 r_scbond_it 2.16 r_angle_refined_deg 1.419 r_mcangle_it 1.309 r_mcbond_it 0.681 r_chiral_restr 0.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.054 r_dihedral_angle_3_deg 10.661 r_dihedral_angle_4_deg 6.751 r_dihedral_angle_1_deg 3.597 r_scangle_it 3.514 r_scbond_it 2.16 r_angle_refined_deg 1.419 r_mcangle_it 1.309 r_mcbond_it 0.681 r_chiral_restr 0.063 r_bond_refined_d 0.009 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 2038 Nucleic Acid Atoms Solvent Atoms 375 Heterogen Atoms 12
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling