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X-ray structure of Melon necrotic spot virus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2TBV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 PEG2000, phosphate buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.09 69.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 375.004 α = 90 b = 375.004 β = 90 c = 375.004 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MACSCIENCE M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.900 SPring-8 BL44XU
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 2.79 267 97 0.164 16.4 208594
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 2.79 2.94 0.608 3.2 9.3
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 2TBV 2.81 187.5 198102 10487 99.2 0.20916 0.20839 0.22373 0.4859 RANDOM 32.452
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.541 r_dihedral_angle_3_deg 19.336 r_dihedral_angle_4_deg 17.938 r_dihedral_angle_1_deg 6.3 r_scangle_it 2.175 r_angle_refined_deg 1.352 r_scbond_it 1.241 r_mcangle_it 0.88 r_mcbond_it 0.502 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.541 r_dihedral_angle_3_deg 19.336 r_dihedral_angle_4_deg 17.938 r_dihedral_angle_1_deg 6.3 r_scangle_it 2.175 r_angle_refined_deg 1.352 r_scbond_it 1.241 r_mcangle_it 0.88 r_mcbond_it 0.502 r_nbtor_refined 0.316 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.207 r_metal_ion_refined 0.172 r_xyhbond_nbd_refined 0.129 r_symmetry_hbond_refined 0.116 r_chiral_restr 0.097 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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_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 7040 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling DM phasing