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Structure of PurE (N5-carboxyaminoimidazole ribonucleotide mutase) from the acidophilic bacterium Acetobacter aceti, complexed with AIR (5-aminoimidazole ribonucleotide)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U11 PDB entry 1U11
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 0.2M lithium sulfate, 0.1M Tris pH 8, 30% (w/v) PEG 4000
(soaked at pH 7), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.68 54.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.199 α = 90 b = 99.199 β = 90 c = 164.389 γ = 90
Symmetry Space Group I 4 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 111 IMAGE PLATE RIGAKU RAXIS IV 2005-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54
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 1.95 40 99.2 0.064 23.4 5.6 30068 -3 17.1
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 1.95 2.02 97.1 0.494 3.6 4.9 2883
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 1U11 1.95 35.46 30068 29092 1229 96 0.191 0.191 0.1906 0.202 0.2022 RANDOM 21.4
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] -0.72 -0.72 1.44
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.1 c_scangle_it 2.72 c_scbond_it 1.95 c_mcangle_it 1.58 c_angle_deg 1.3 c_mcbond_it 1.07 c_improper_angle_d 0.86 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.1 c_scangle_it 2.72 c_scbond_it 1.95 c_mcangle_it 1.58 c_angle_deg 1.3 c_mcbond_it 1.07 c_improper_angle_d 0.86 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot 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 2307 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 19
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing