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Crystal structures of 5-aminoimidazole ribonucleotide (AIR) synthetase, PurM, from Thermus thermophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BTU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 1.0 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 3.92 68.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.328 α = 90 b = 142.63 β = 90 c = 218.616 γ = 90
Symmetry Space Group P 21 21 2
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 RIGAKU JUPITER 210 2004-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
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 50 99.6 0.087 17.4 6.5 224495
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) 1 2.2 2.28 98.5 0.288 4.5 5.7
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 2BTU 2.2 50 217248 20886 96.6 0.163 0.163 0.1608 0.215 0.2106 RANDOM 30.32
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] -0.114 -0.391 0.504
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.68 c_scangle_it 2.725 c_scbond_it 1.791 c_mcangle_it 1.765 c_angle_d 1.318 c_mcbond_it 1.065 c_improper_angle_d 0.889 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.68 c_scangle_it 2.725 c_scbond_it 1.791 c_mcangle_it 1.765 c_angle_d 1.318 c_mcbond_it 1.065 c_improper_angle_d 0.889 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d_na c_angle_d_prot c_angle_deg c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16868 Nucleic Acid Atoms Solvent Atoms 1767 Heterogen Atoms 85
Software Software Software Name Purpose CNS refinement HKL-2000 data processing HKL-2000 data scaling AMoRE phasing HKL-2000 data reduction