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Crystal structure of IGPD from Pyrococcus furiosus in complex with (S)-C348
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F1D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 290 0.1M MES buffer pH 6 and 10% MPD
Crystal Properties Matthews coefficient Solvent content 2.89 57.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.27 α = 90 b = 141.27 β = 90 c = 137.41 γ = 90
Symmetry Space Group I 4 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 2012-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
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 1.53 49.25 100 0.08 18.1 13.1 103816
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 1.53 1.57 100 0.688 4.1 13.2
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 2F1D 1.53 49.25 98527 5289 99.88 0.13557 0.13484 0.1498 0.14916 0.1619 RANDOM 19.679
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] -0.09 -0.09 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.601 r_scbond_it 23.206 r_scbond_other 23.2 r_dihedral_angle_4_deg 19.178 r_scangle_other 16.468 r_long_range_B_refined 15.031 r_long_range_B_other 15.03 r_dihedral_angle_3_deg 10.616 r_dihedral_angle_1_deg 6.369 r_mcbond_it 5.931
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.601 r_scbond_it 23.206 r_scbond_other 23.2 r_dihedral_angle_4_deg 19.178 r_scangle_other 16.468 r_long_range_B_refined 15.031 r_long_range_B_other 15.03 r_dihedral_angle_3_deg 10.616 r_dihedral_angle_1_deg 6.369 r_mcbond_it 5.931 r_mcangle_other 5.629 r_mcangle_it 4.596 r_mcbond_other 2.971 r_angle_refined_deg 1.473 r_angle_other_deg 0.863 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4164 Nucleic Acid Atoms Solvent Atoms 476 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing