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Crystal structure of PurP from Pyrococcus furiosus complexed with AMP and AICAR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R7K PDB entry 2R7K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 30% MPD, 200 mM NaCl, 100 mM Tris, pH 7.0, vapor diffusion, hanging drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.6 65.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.671 α = 90 b = 123.671 β = 90 c = 375.359 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 2006-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97918 APS 24-ID-C
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 1.9 50 99.3 0.074 9.1 7 85987 85981
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 1.9 1.97 94.4 0.365 5.9 8102
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 PDB entry 2R7K 1.9 37.9 85987 85981 4365 99.16 0.175 0.175 0.174 0.1731 0.195 0.1925 RANDOM 21.777
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] 0.68 0.34 0.68 -1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.296 r_dihedral_angle_3_deg 12.298 r_dihedral_angle_4_deg 11.573 r_dihedral_angle_1_deg 5.334 r_scangle_it 1.671 r_angle_refined_deg 1.072 r_scbond_it 0.958 r_mcangle_it 0.667 r_mcbond_it 0.342 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.296 r_dihedral_angle_3_deg 12.298 r_dihedral_angle_4_deg 11.573 r_dihedral_angle_1_deg 5.334 r_scangle_it 1.671 r_angle_refined_deg 1.072 r_scbond_it 0.958 r_mcangle_it 0.667 r_mcbond_it 0.342 r_nbtor_refined 0.3 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.146 r_symmetry_hbond_refined 0.093 r_xyhbond_nbd_refined 0.091 r_metal_ion_refined 0.075 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5215 Nucleic Acid Atoms Solvent Atoms 624 Heterogen Atoms 118
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling