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Structure of N-terminally truncated A49 from Vaccinia Virus Western Reserve
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D5R PDB ENTRY 4D5R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 293 PROTEIN (1 UL AT 25.0 MG/ML) WAS MIXED WITH 1 UL RESERVOIR SOLUTION AND EQUILIBRATED AT 20 C AGAINST 500 UL RESERVOIRS CONTAINING 0.1 M HEPES PH 7.5, 1.6 M AMMONIUM SULFATE AND 1.5% (VOL/VOL) PEG 400. CRYSTALS WERE CRYOPROTECTED BY PASSAGE THROUGH 2 UL OF PERFLUOROPOLYETHER OIL (HAMPTON RESEARCH) THAT HAD BEEN OVERLAID ONTO THE MOTHER LIQUOR.
Crystal Properties Matthews coefficient Solvent content 2.26 45.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.29 α = 90 b = 45.63 β = 98.74 c = 160.26 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 PIXEL DECTRIS PILATUS 2M TOROIDAL MIRRORS 2013-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 1.84 45.7 97.9 0.07 13.6 6.8 112855 -3 21.6
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 1.84 1.89 96 1.16 1.5 6.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4D5R 1.84 45.71 107126 5665 97.61 0.20801 0.20638 0.23888 0.2411 RANDOM 36.864
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] -2.12 0.82 0.49 1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.482 r_dihedral_angle_4_deg 16.898 r_dihedral_angle_3_deg 13.285 r_dihedral_angle_1_deg 5.509 r_scbond_it 2.998 r_mcangle_it 2.868 r_mcbond_it 2.06 r_mcbond_other 2.06 r_angle_other_deg 1.988 r_angle_refined_deg 1.689
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.482 r_dihedral_angle_4_deg 16.898 r_dihedral_angle_3_deg 13.285 r_dihedral_angle_1_deg 5.509 r_scbond_it 2.998 r_mcangle_it 2.868 r_mcbond_it 2.06 r_mcbond_other 2.06 r_angle_other_deg 1.988 r_angle_refined_deg 1.689 r_chiral_restr 0.104 r_bond_refined_d 0.017 r_bond_other_d 0.014 r_gen_planes_refined 0.012 r_gen_planes_other 0.01 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9714 Nucleic Acid Atoms Solvent Atoms 894 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing