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Nipah Virus Attachment Glycoprotein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VSM PDB ENTRY 2VSM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 20% (V/V) PEG 6000, 0.1 M MES PH 6.0, 0.1 M LICL AND 0.1 M GAMMA-BUTYLACTONE 18%
Crystal Properties Matthews coefficient Solvent content 2.7 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.633 α = 90 b = 86.936 β = 108.32 c = 82.903 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 77.2 CCD MARMOSAIC 225 mm CCD MIRRORS 2007-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 2.25 40 100 0.14 18.4 7.3 45810 -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 2.25 2.33 100 0.87 3 5.8
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 2VSM 2.25 39.94 43463 2323 99.8 0.175 0.172 0.221 0.2237 RANDOM 21.73
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] 0.39 0.08 0.86 -1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.138 r_dihedral_angle_4_deg 15.875 r_dihedral_angle_3_deg 13.018 r_dihedral_angle_1_deg 6.334 r_scangle_it 1.611 r_angle_refined_deg 1.209 r_scbond_it 0.988 r_angle_other_deg 0.839 r_mcangle_it 0.705 r_mcbond_it 0.642
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.138 r_dihedral_angle_4_deg 15.875 r_dihedral_angle_3_deg 13.018 r_dihedral_angle_1_deg 6.334 r_scangle_it 1.611 r_angle_refined_deg 1.209 r_scbond_it 0.988 r_angle_other_deg 0.839 r_mcangle_it 0.705 r_mcbond_it 0.642 r_nbd_other 0.184 r_nbd_refined 0.175 r_nbtor_refined 0.171 r_symmetry_vdw_other 0.159 r_symmetry_vdw_refined 0.147 r_xyhbond_nbd_refined 0.135 r_symmetry_hbond_refined 0.132 r_nbtor_other 0.093 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 6510 Nucleic Acid Atoms Solvent Atoms 578 Heterogen Atoms 190
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing