☰ Navigation Tabs
Crystal Structure of H2Db in complex with NP366-N3A variant peptide from influenza
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CPL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 0.2M lithium sulfate, 28% PEG 3350, 0.1M sodium citrate, pH 5.6, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.24 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.64 α = 90 b = 94.98 β = 90 c = 132.24 γ = 90
Symmetry Space Group I 2 2 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 IMAGE PLATE RIGAKU RAXIS IV MIRRORS 2007-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.6 20 98.7 0.06 27.55 7.22 18264 -3 47.68
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 2.6 2.7 97.7 0.303 6.4 6.93 1905
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3CPL 2.6 15 18178 1857 98.89 0.229 0.221 0.2225 0.304 0.3022 RANDOM 40.807
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] -0.45 -0.17 0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.413 r_dihedral_angle_3_deg 20.701 r_dihedral_angle_4_deg 19.5 r_dihedral_angle_1_deg 7.048 r_scangle_it 2.037 r_angle_refined_deg 1.468 r_scbond_it 1.346 r_mcangle_it 1.216 r_mcbond_it 0.686 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.413 r_dihedral_angle_3_deg 20.701 r_dihedral_angle_4_deg 19.5 r_dihedral_angle_1_deg 7.048 r_scangle_it 2.037 r_angle_refined_deg 1.468 r_scbond_it 1.346 r_mcangle_it 1.216 r_mcbond_it 0.686 r_nbtor_refined 0.308 r_nbd_refined 0.232 r_symmetry_vdw_refined 0.231 r_symmetry_hbond_refined 0.225 r_xyhbond_nbd_refined 0.19 r_chiral_restr 0.099 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2936 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection XDS data reduction