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The Crystal Structure of Cypovirus Polyhedra containing the Human ZIP-kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OH6 PDB entry 2OH6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 300 The crystals used to determine this structure were directly purified from cells, in vivo crystallization in the cytoplasm of the cell, temperature 300K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.742 α = 90 b = 102.742 β = 90 c = 102.742 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD MAR CCD 165 mm MD2 diffractometer 2006-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.99830 SLS X06SA
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 2.45 20 99.9 0.128 8.2 8.2 6778 6770 -3 23.4
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) 2.45 2.54 99.4 0.348 3.7 3.5 656
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 2OH6 2.45 18.8 6744 6736 644 99.88 0.122 0.122 0.112 0.1258 0.221 0.2247 RANDOM 17.933
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.486 r_dihedral_angle_4_deg 24.078 r_dihedral_angle_3_deg 13.976 r_dihedral_angle_1_deg 7.383 r_scangle_it 2.475 r_angle_refined_deg 1.68 r_scbond_it 1.667 r_mcangle_it 0.947 r_angle_other_deg 0.944 r_mcbond_it 0.713
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.486 r_dihedral_angle_4_deg 24.078 r_dihedral_angle_3_deg 13.976 r_dihedral_angle_1_deg 7.383 r_scangle_it 2.475 r_angle_refined_deg 1.68 r_scbond_it 1.667 r_mcangle_it 0.947 r_angle_other_deg 0.944 r_mcbond_it 0.713 r_symmetry_vdw_other 0.22 r_symmetry_hbond_refined 0.21 r_nbd_other 0.198 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.188 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.16 r_mcbond_other 0.141 r_chiral_restr 0.094 r_nbtor_other 0.088 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2007 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 95
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction