☰ Navigation Tabs
Crystal structure of Phosphoribosylaminoimidazolecarboxamide formyltransferase / IMP cyclohydrolase (TM1249) from THERMOTOGA MARITIMA at 1.88 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M9N 1m9n 1g8mA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 5 293 20.0% PEG-6000, 0.1M Citrate pH 5.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 46.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.084 α = 99.26 b = 58.63 β = 96.89 c = 72.749 γ = 106.13
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 210 Single crystal, cylindrically bent, Si(220) 2005-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 ALS 5.0.1
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 1.88 50 95.6 0.056 25.65 2.9 74289
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 1.88 1.91 70.6 70.6 0.314 0.0205 1.6
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 (All) 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 1m9n 1g8mA 1.88 50 69797 3700 95.89 0.158 0.15849 0.156 0.1663 0.197 0.2069 RANDOM 36.497
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] -1.56 -0.09 -1.16 0.21 -1.07 0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.025 r_dihedral_angle_4_deg 16.251 r_dihedral_angle_3_deg 13.86 r_scangle_it 6.267 r_dihedral_angle_1_deg 5.785 r_scbond_it 4.296 r_mcangle_it 2.577 r_mcbond_it 1.603 r_angle_refined_deg 1.395 r_angle_other_deg 0.985
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.025 r_dihedral_angle_4_deg 16.251 r_dihedral_angle_3_deg 13.86 r_scangle_it 6.267 r_dihedral_angle_1_deg 5.785 r_scbond_it 4.296 r_mcangle_it 2.577 r_mcbond_it 1.603 r_angle_refined_deg 1.395 r_angle_other_deg 0.985 r_mcbond_other 0.615 r_symmetry_vdw_other 0.263 r_metal_ion_refined 0.223 r_nbd_refined 0.22 r_nbd_other 0.178 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.155 r_symmetry_hbond_refined 0.098 r_chiral_restr 0.087 r_nbtor_other 0.084 r_symmetry_vdw_refined 0.071 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6961 Nucleic Acid Atoms Solvent Atoms 636 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction DENZO data reduction