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Crystal Structure of purK: N5-carboxyaminoimidazole ribonucleotide synthetase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K5I homology model of 3K5I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.1M MES, 5mM DTT, 9% glycerol, 10% PEG6000, Hampton Research Silver Bullet Bio additive B5/17, pH 6.5, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.28 46.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.43 α = 90 b = 82.445 β = 90 c = 166.621 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 CCD MARMOSAIC 300 mm CCD 2010-12-02 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 2010-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00 APS 22-ID 2 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9791 APS 24-ID-E
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 1.96 20 96.9 0.106 14.67 7.6 56242 56242 -3 -3 34.171
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 1.96 2.07 81.3 0.75 2.7 4.9 7484
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 (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 homology model of 3K5I 1.96 19.96 53364 53364 2848 97.08 0.1973 0.1973 0.1952 0.1961 0.2352 0.2337 RANDOM 28.5343
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.207 r_dihedral_angle_3_deg 13.967 r_dihedral_angle_4_deg 12.728 r_dihedral_angle_1_deg 5.341 r_scangle_it 2.93 r_scbond_it 1.686 r_mcangle_it 1.233 r_angle_refined_deg 1.109 r_mcbond_it 0.655 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.207 r_dihedral_angle_3_deg 13.967 r_dihedral_angle_4_deg 12.728 r_dihedral_angle_1_deg 5.341 r_scangle_it 2.93 r_scbond_it 1.686 r_mcangle_it 1.233 r_angle_refined_deg 1.109 r_mcbond_it 0.655 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5876 Nucleic Acid Atoms Solvent Atoms 379 Heterogen Atoms 2
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection XDS data reduction XDS data scaling