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Merkel cell polyomavirus VP1 in complex with GD1a oligosaccharide
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 25 mM GD1a oligosaccharide, cryoprotection: 25% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.64 53.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.66 α = 98.04 b = 130.15 β = 101.02 c = 165.53 γ = 105.81
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 PIXEL PSI PILATUS 6M 2010-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000 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 2.4 50 97.3 0.101 8.74 3.6 255632 248679 -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 2.4 2.46 96.8 0.666 2.07 3.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.4 50 242479 6193 97.33 0.19297 0.19162 0.24623 0.233 RANDOM 38.97
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] 2.61 -1.06 0.17 -2.22 -1.14 -1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.002 r_dihedral_angle_4_deg 17.605 r_dihedral_angle_3_deg 14.917 r_dihedral_angle_1_deg 5.75 r_scangle_it 4.231 r_scbond_it 2.755 r_mcangle_it 2.076 r_angle_refined_deg 1.112 r_mcbond_it 1.105 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.002 r_dihedral_angle_4_deg 17.605 r_dihedral_angle_3_deg 14.917 r_dihedral_angle_1_deg 5.75 r_scangle_it 4.231 r_scbond_it 2.755 r_mcangle_it 2.076 r_angle_refined_deg 1.112 r_mcbond_it 1.105 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 42561 Nucleic Acid Atoms Solvent Atoms 1568 Heterogen Atoms 281
Software Software Software Name Purpose RemDAq data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling