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Crystal structure of PurP from Pyrococcus furiosus complexed with ATP
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 6.1 291 30% MPD, 100 mM Na/K phosphate, pH 6.1, vapor diffusion, hanging drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 5.28 76.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.477 α = 90 b = 122.477 β = 90 c = 560.925 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 2.5 50 97.9 0.057 11.6 7.5 55984 55970
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) 2.5 2.59 81.9 0.283 6.1 4588
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 2.5 39.97 55984 55970 2874 97.84 0.219 0.219 0.218 0.2067 0.239 0.2255 RANDOM 47.904
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] 1.86 0.93 1.86 -2.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.099 r_dihedral_angle_3_deg 14.795 r_dihedral_angle_4_deg 11.642 r_dihedral_angle_1_deg 5.628 r_scangle_it 1.676 r_angle_refined_deg 1.024 r_scbond_it 0.94 r_mcangle_it 0.87 r_mcbond_it 0.463 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.099 r_dihedral_angle_3_deg 14.795 r_dihedral_angle_4_deg 11.642 r_dihedral_angle_1_deg 5.628 r_scangle_it 1.676 r_angle_refined_deg 1.024 r_scbond_it 0.94 r_mcangle_it 0.87 r_mcbond_it 0.463 r_nbtor_refined 0.305 r_nbd_refined 0.18 r_symmetry_vdw_refined 0.152 r_symmetry_hbond_refined 0.139 r_xyhbond_nbd_refined 0.103 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5302 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 84
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