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Structure of 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 1 294 FULL-LENGTH A49 (100 NL AT 9.5 MG/ML) WAS MIXED WITH 100 NL RESERVOIR SOLUTION AND EQUILIBRATED AT 21 C AGAINST 95 UL RESERVOIRS COMPRISING 25% (WT/VOL) PEG 3350, 0.2 M AMMONIUM SULFATE AND 0.1 M TRIS PH 9.5. CRYOPROTECTION WAS ACHIEVED BY QUICKLY SWEEPING THE CRYSTAL THROUGH RESERVOIR SUPPLEMENTED WITH 20% (VOL/VOL) GLYCEROL.
Crystal Properties Matthews coefficient Solvent content 2.22 44.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.783 α = 90 b = 67.783 β = 90 c = 153.947 γ = 90
Symmetry Space Group P 43 21 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 CCD ADSC QUANTUM 4 TOROIDAL ZERODUR MIRROR 2008-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 3 50 100 0.1 17.5 13.8 7353 -3 81.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.05 100 2.2 14.4
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 3 153.95 7350 356 99.91 0.22215 0.21987 0.27332 0.2583 RANDOM 94.958
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] 2.09 2.09 -4.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.254 r_dihedral_angle_4_deg 16.5 r_dihedral_angle_3_deg 13.934 r_dihedral_angle_1_deg 6.714 r_mcangle_it 5.782 r_scbond_it 4.126 r_mcbond_it 3.611 r_mcbond_other 3.605 r_angle_refined_deg 1.37 r_angle_other_deg 0.832
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.254 r_dihedral_angle_4_deg 16.5 r_dihedral_angle_3_deg 13.934 r_dihedral_angle_1_deg 6.714 r_mcangle_it 5.782 r_scbond_it 4.126 r_mcbond_it 3.611 r_mcbond_other 3.605 r_angle_refined_deg 1.37 r_angle_other_deg 0.832 r_chiral_restr 0.071 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 2292 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing