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Structure of PIN-domain protein (VapC4 toxin) from Pyrococcus horikoshii determined at 2.2 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
Crystal Properties Matthews coefficient Solvent content 1.77 30.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.97 α = 90 b = 45.26 β = 104.75 c = 53.62 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 2011-01-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU ULTRAX 18 1.54179
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 2.21 51.85 97.2 8.5 3.3 11886
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 2.21 2.29 71.2 0.42 0.54 2.4 3
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 2.23 51.85 11212 661 99.64 0.21012 0.20707 0.2122 0.25904 0.2608 RANDOM 28.159
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] 0.81 -0.76 0.94 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.502 r_dihedral_angle_4_deg 20.927 r_dihedral_angle_3_deg 14.773 r_dihedral_angle_1_deg 5.615 r_long_range_B_refined 3.09 r_long_range_B_other 3.088 r_scangle_other 1.942 r_mcangle_it 1.777 r_mcangle_other 1.776 r_angle_refined_deg 1.236
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.502 r_dihedral_angle_4_deg 20.927 r_dihedral_angle_3_deg 14.773 r_dihedral_angle_1_deg 5.615 r_long_range_B_refined 3.09 r_long_range_B_other 3.088 r_scangle_other 1.942 r_mcangle_it 1.777 r_mcangle_other 1.776 r_angle_refined_deg 1.236 r_scbond_it 1.134 r_scbond_other 1.133 r_mcbond_it 1.044 r_mcbond_other 1.041 r_angle_other_deg 0.909 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2285 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing