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Crystal structure of Phospho-2-dehydro-3-deoxyheptonate aldolase (DAHP synthase) (TM0343) from Thermotoga Maritima at 1.92 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RZM PDB entry 1RZM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP, NANODROP 5.5 293 35.0% Ethylene-Glycol, 0.1M Acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 43.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.151 α = 90 b = 74.226 β = 90 c = 249.54 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 100 CCD ADSC QUANTUM 315 fixed-height exit beam, toroidal focusing mirror 2004-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.92 47.76 98.79 0.065 23.07 3.57 102464 44.73
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 1.96 90.38 0.659 1.49 2.63 4594
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 1RZM 1.92 47.76 97241 5111 98.54 0.1732 0.17089 0.1793 0.21519 0.2238 RANDOM 42.205
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] 0.01 -0.29 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.389 r_dihedral_angle_4_deg 20.19 r_dihedral_angle_3_deg 14.676 r_scangle_it 7.058 r_dihedral_angle_1_deg 5.943 r_scbond_it 5.247 r_mcangle_it 3.095 r_mcbond_it 2.113 r_angle_refined_deg 1.516 r_angle_other_deg 0.842
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.389 r_dihedral_angle_4_deg 20.19 r_dihedral_angle_3_deg 14.676 r_scangle_it 7.058 r_dihedral_angle_1_deg 5.943 r_scbond_it 5.247 r_mcangle_it 3.095 r_mcbond_it 2.113 r_angle_refined_deg 1.516 r_angle_other_deg 0.842 r_mcbond_other 0.604 r_symmetry_vdw_other 0.298 r_symmetry_vdw_refined 0.271 r_nbd_refined 0.213 r_nbd_other 0.192 r_xyhbond_nbd_refined 0.18 r_symmetry_hbond_refined 0.179 r_nbtor_refined 0.172 r_chiral_restr 0.093 r_nbtor_other 0.086 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10375 Nucleic Acid Atoms Solvent Atoms 615 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement