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Crystal Structure of Shikimate Dehydrogenase (aroE) Clinical Variant v2356 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 293 1.5M ammonium sulfate, 1.0M lithium sulfate, 0.1M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.3 62.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.118 α = 90 b = 71.87 β = 90 c = 176.388 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 315 mirrors 2012-06-05 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) 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 2.85 30 99.9 0.072 15 8.2 19482
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 2.85 2.95 100 0.464 4.9 8.5 1891
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 3PHG 2.85 30 19324 971 99.52 0.2166 0.2143 0.2112 0.26 0.222 RANDOM 67.7202
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] 2.51 3.74 -6.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.211 r_dihedral_angle_4_deg 24.916 r_dihedral_angle_3_deg 23.778 r_dihedral_angle_1_deg 7.603 r_scangle_it 4.573 r_scbond_it 2.618 r_mcangle_it 2.015 r_angle_refined_deg 1.312 r_mcbond_it 1.031 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.211 r_dihedral_angle_4_deg 24.916 r_dihedral_angle_3_deg 23.778 r_dihedral_angle_1_deg 7.603 r_scangle_it 4.573 r_scbond_it 2.618 r_mcangle_it 2.015 r_angle_refined_deg 1.312 r_mcbond_it 1.031 r_chiral_restr 0.098 r_bond_refined_d 0.017 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4097 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 12
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing