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Crystal structure of the West Nile virus envelope glycoprotein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZTX PDB ENTRIES 1ZTX, 1UZG AND 1OAN experimental model PDB 1UZG PDB ENTRIES 1ZTX, 1UZG AND 1OAN experimental model PDB 1OAN PDB ENTRIES 1ZTX, 1UZG AND 1OAN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 293 15% (v/v) isopropanol, 0.1 M HEPES pH 7.5, and 0.2 M Na citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 3.99 69.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.262 α = 90 b = 93.262 β = 90 c = 159.319 γ = 90
Symmetry Space Group P 41 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 DOUBLY FOCUSING TOROIDAL MIRROR 2006-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C NSLS X26C
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 3.11 25 94.7 0.111 14.62 8.1 13289 86.6
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 3.11 3.23 96.4 0.721 2.48 8.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRIES 1ZTX, 1UZG AND 1OAN 3.11 24.06 13883 11858 618 94.8 0.209 0.206 0.2037 0.268 0.2602 RANDOM 117.633
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] 0.79 0.79 -1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.385 r_dihedral_angle_3_deg 23.105 r_dihedral_angle_4_deg 20.159 r_dihedral_angle_1_deg 7.35 r_scangle_it 5.286 r_mcangle_it 5.142 r_scbond_it 3.378 r_mcbond_it 3.169 r_angle_refined_deg 1.676 r_nbtor_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.385 r_dihedral_angle_3_deg 23.105 r_dihedral_angle_4_deg 20.159 r_dihedral_angle_1_deg 7.35 r_scangle_it 5.286 r_mcangle_it 5.142 r_scbond_it 3.378 r_mcbond_it 3.169 r_angle_refined_deg 1.676 r_nbtor_refined 0.321 r_symmetry_vdw_refined 0.253 r_nbd_refined 0.248 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.107 r_symmetry_hbond_refined 0.049 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 3043 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing