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Structural characterization of the Ppx/GppA protein family: crystal structure of the Aquifex aeolicus family member
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other A very incomplete model was obtained through experimental phasing and Arp/Warp tracing of the Type II crystal form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 293 MPD, MES, TRIS, KCl, DTT, The crystal was soaked in K2HgI4/KI containing solution, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 46.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.776 α = 90 b = 70.287 β = 90 c = 90.783 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 IMAGE PLATE MARRESEARCH 2000-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 0.993 MAX II I711
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 1.53 15 95.8 0.069 0.061 22.8 6.9 47505 47505 19
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 1.53 1.61 84.6 0.341 0.24 2.2 2.7 5936
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 with partial model, followed by the Arp/Warp procedure. THROUGHOUT A very incomplete model was obtained through experimental phasing and Arp/Warp tracing of the Type II crystal form 1.53 15 47463 46991 472 95.6 0.162 0.162 0.1658 0.217 0.2208 RANDOM 16.249
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] -0.88 -1 1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.188 r_scangle_it 4.485 r_scbond_it 2.617 r_mcangle_it 1.698 r_angle_refined_deg 1.494 r_mcbond_it 0.879 r_angle_other_deg 0.85 r_symmetry_vdw_other 0.298 r_nbd_other 0.24 r_symmetry_hbond_refined 0.226
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.188 r_scangle_it 4.485 r_scbond_it 2.617 r_mcangle_it 1.698 r_angle_refined_deg 1.494 r_mcbond_it 0.879 r_angle_other_deg 0.85 r_symmetry_vdw_other 0.298 r_nbd_other 0.24 r_symmetry_hbond_refined 0.226 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.175 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.087 r_nbtor_other 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2456 Nucleic Acid Atoms Solvent Atoms 390 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling CNS phasing ARP/wARP model building