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Crystal structure of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase) from Aeropyrum pernix in complex with Mn2+ and PEP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RZM FRAGMENT OF PDB ENTRY 1RZM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1 M HEPES, 0.2 M lithium sulfate, 0.2 M magnesium chloride, 30% v/v 2-propanol, 10% v/v butanol
Crystal Properties Matthews coefficient Solvent content 2.18 43.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.768 α = 90 b = 130.404 β = 110.61 c = 78.362 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 MARMOSAIC 225 mm CCD 2004-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 0.92015 APS 22-BM
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 2.2 90.7 90.7 0.093 19.2 7.4 47755 47755 -3
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) 2.2 2.28 46 0.344 8.6 6.1 2403
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 FRAGMENT OF PDB ENTRY 1RZM 2.3 20 47755 41839 2246 96.54 0.17562 0.17329 0.1741 0.21754 0.2175 RANDOM 36.141
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] 2.01 -0.69 -3.48 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.08 r_dihedral_angle_4_deg 19.506 r_dihedral_angle_3_deg 16.422 r_scangle_it 7.296 r_scbond_it 5.721 r_dihedral_angle_1_deg 5.605 r_mcangle_it 2.844 r_angle_refined_deg 1.666 r_mcbond_it 1.644 r_symmetry_hbond_refined 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.08 r_dihedral_angle_4_deg 19.506 r_dihedral_angle_3_deg 16.422 r_scangle_it 7.296 r_scbond_it 5.721 r_dihedral_angle_1_deg 5.605 r_mcangle_it 2.844 r_angle_refined_deg 1.666 r_mcbond_it 1.644 r_symmetry_hbond_refined 0.47 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.268 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.108 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 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 8187 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SHELXD phasing SHELXE model building MLPHARE phasing DM phasing SOLVE phasing RESOLVE phasing O model building Coot model building CCP4 phasing