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Merkel Cell Polyomavirus VP1 in complex with Disialyllactose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M sodium cacodylate, pH 6.5, 6% w/v PEG3350, 0.3 M magnesium chloride, soaked in 20 mM disialyllactose, cryoprotection: 25% w/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.65 53.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.27 α = 92.97 b = 85.77 β = 100.48 c = 248.71 γ = 108.05
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD MARMOSAIC 225 mm CCD 2010-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000 SLS X06DA
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 1.85 50 94.7 0.096 9.52 3.3 558787 529047 -3
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 1.85 1.9 90 0.612 1.74 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.85 50 523737 5310 94.68 0.16595 0.16564 0.1661 0.19575 0.195 RANDOM 20.148
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] 0.66 0.28 -0.05 0.31 -0.15 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.519 r_dihedral_angle_4_deg 19.296 r_dihedral_angle_3_deg 12.676 r_dihedral_angle_1_deg 5.923 r_scangle_it 4.27 r_scbond_it 2.755 r_mcangle_it 1.855 r_angle_refined_deg 1.108 r_mcbond_it 1.019 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.519 r_dihedral_angle_4_deg 19.296 r_dihedral_angle_3_deg 12.676 r_dihedral_angle_1_deg 5.923 r_scangle_it 4.27 r_scbond_it 2.755 r_mcangle_it 1.855 r_angle_refined_deg 1.108 r_mcbond_it 1.019 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 42808 Nucleic Acid Atoms Solvent Atoms 4560 Heterogen Atoms 580
Software Software Software Name Purpose RemDAq data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling