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Crystal structure of PurP from Pyrococcus furiosus complexed with ADP
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 4.2 291 10% 2-propanol, 200 mM Li2SO4, 100 mM Na phosphate-citrate, pH 4.2, vapor diffusion, hanging drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.5 50.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.095 α = 90 b = 127.222 β = 102.85 c = 121.673 γ = 90
Symmetry Space Group P 1 21 1
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 270 2007-01-01 M SINGLE WAVELENGTH 2 1 IMAGE PLATE RIGAKU RAXIS IV 2007-05-05
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.91770 CHESS F1 2 ROTATING ANODE RIGAKU 1.54178
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 2.3 50 98.8 0.138 8.7 4.4 98989 98928
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) 2.3 2.38 98.5 0.264 2.9 9860
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 2.3 42.64 98989 98928 4941 98.67 0.203 0.203 0.201 0.2003 0.244 0.2421 RANDOM 22.251
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] 0.37 -1.66 -1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.627 r_dihedral_angle_3_deg 14.87 r_dihedral_angle_4_deg 9.23 r_dihedral_angle_1_deg 5.711 r_scangle_it 1.414 r_angle_refined_deg 1.067 r_scbond_it 0.827 r_mcangle_it 0.735 r_mcbond_it 0.419 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.627 r_dihedral_angle_3_deg 14.87 r_dihedral_angle_4_deg 9.23 r_dihedral_angle_1_deg 5.711 r_scangle_it 1.414 r_angle_refined_deg 1.067 r_scbond_it 0.827 r_mcangle_it 0.735 r_mcbond_it 0.419 r_nbtor_refined 0.302 r_nbd_refined 0.175 r_symmetry_vdw_refined 0.153 r_xyhbond_nbd_refined 0.117 r_symmetry_hbond_refined 0.098 r_chiral_restr 0.074 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16230 Nucleic Acid Atoms Solvent Atoms 541 Heterogen Atoms 257
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