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Crystal structure of enzyme in purine metabolism
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J2C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 100 mM MES/imidazol containing 200 mM NaCl, 30 % glycerol and 10 % PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.94 58.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.519 α = 90 b = 126.541 β = 90 c = 130.32 γ = 90
Symmetry Space Group I 2 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 100 PIXEL DECTRIS PILATUS 6M 2014-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.738 48.948 98.2 0.053 20.1 5.2 76477 36.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.738 1.747 89.6 0.707 1.9 3.7
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 2J2C 1.79 48.33 67541 3555 99.33 0.1717 0.1706 0.1804 0.1924 0.2017 RANDOM 33.887
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] -0.34 0.48 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.071 r_dihedral_angle_4_deg 15.88 r_dihedral_angle_3_deg 13.714 r_dihedral_angle_1_deg 5.906 r_angle_refined_deg 1.472 r_mcangle_it 1.398 r_angle_other_deg 0.943 r_mcbond_it 0.85 r_mcbond_other 0.842 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.071 r_dihedral_angle_4_deg 15.88 r_dihedral_angle_3_deg 13.714 r_dihedral_angle_1_deg 5.906 r_angle_refined_deg 1.472 r_mcangle_it 1.398 r_angle_other_deg 0.943 r_mcbond_it 0.85 r_mcbond_other 0.842 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3843 Nucleic Acid Atoms Solvent Atoms 344 Heterogen Atoms 42
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Coot model building