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Structure of PIN-domain protein (VapC4 toxin) from Pyrococcus horikoshii determined at 1.77 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V96
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 0.2M Sodium acetate trihydrate, 0.1M Tris-HCl, 30%(w/v) PEG 4000, 0.1M Turine
Crystal Properties Matthews coefficient Solvent content 1.68 26.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.78 α = 90 b = 44.64 β = 103.4 c = 52.37 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 300 CCD MARMOSAIC 225 mm CCD 2011-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97625 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.77 50.94 99.1 18.4 7.2 22115
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.81 97.1 0.749 0.68 2.3 6.2
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 1V96 1.77 50.94 20988 1113 98.78 0.17001 0.16737 0.1768 0.22135 0.2277 RANDOM 27.634
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] 0.24 -0.86 0.41 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.12 r_dihedral_angle_4_deg 20.73 r_dihedral_angle_3_deg 14.44 r_long_range_B_refined 6.785 r_long_range_B_other 6.756 r_dihedral_angle_1_deg 5.908 r_scangle_other 5.195 r_mcangle_other 3.727 r_mcangle_it 3.723 r_scbond_other 3.576
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.12 r_dihedral_angle_4_deg 20.73 r_dihedral_angle_3_deg 14.44 r_long_range_B_refined 6.785 r_long_range_B_other 6.756 r_dihedral_angle_1_deg 5.908 r_scangle_other 5.195 r_mcangle_other 3.727 r_mcangle_it 3.723 r_scbond_other 3.576 r_scbond_it 3.575 r_mcbond_it 2.591 r_mcbond_other 2.58 r_angle_refined_deg 1.899 r_angle_other_deg 1.078 r_chiral_restr 0.116 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 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 2199 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing