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Thiazole synthase Thi4 from Methanocaldococcus jannaschii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RP0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 9.5 295 1.05 M Potassium/sodium tartrate,
0.1 M CHES/ Sodium hydroxide pH 9.5,
0.2 M Lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.76 60.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.76 α = 90 b = 180.76 β = 90 c = 73.328 γ = 120
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 2012-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9791 APS 24-ID-C
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 2.7 40 99.3 0.072 0.072 13.3 3.5 72800
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 1RP0 2.71 40 68627 3646 99.01 0.17841 0.17708 0.1796 0.20311 0.2017 RANDOM 54.853
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] 0.81 0.4 0.81 -2.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.608 r_dihedral_angle_4_deg 20.202 r_dihedral_angle_3_deg 16.322 r_long_range_B_refined 9.971 r_long_range_B_other 9.971 r_scangle_other 6.613 r_dihedral_angle_1_deg 6.054 r_mcangle_it 4.525 r_mcangle_other 4.525 r_scbond_it 4.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.608 r_dihedral_angle_4_deg 20.202 r_dihedral_angle_3_deg 16.322 r_long_range_B_refined 9.971 r_long_range_B_other 9.971 r_scangle_other 6.613 r_dihedral_angle_1_deg 6.054 r_mcangle_it 4.525 r_mcangle_other 4.525 r_scbond_it 4.143 r_scbond_other 4.143 r_angle_other_deg 3.659 r_mcbond_it 2.963 r_mcbond_other 2.962 r_angle_refined_deg 1.361 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_gen_planes_other 0.004 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15270 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 353
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing