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Tailspike protein mutant D339N of E. coli bacteriophage HK620
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XM3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.1 M Tris-HCl, 3.5 M Sodium formate
Crystal Properties Matthews coefficient Solvent content 2.14 42.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.917 α = 90 b = 73.917 β = 90 c = 174.502 γ = 120
Symmetry Space Group P 3 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M mirrors 2014-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.1 43.05 80.1 0.08 0.043 0.995 10.1 3.5 26540
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 75.7 0.202 0.116 0.936 4.2 2.9 1994
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 4xm3 2.1 43.05 26530 1354 80.09 0.2296 0.2267 0.2314 0.2819 0.2921 RANDOM 22.591
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] 0.63 0.32 0.63 -2.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.639 r_dihedral_angle_4_deg 16.798 r_dihedral_angle_3_deg 12.439 r_dihedral_angle_1_deg 6.267 r_angle_refined_deg 0.998 r_angle_other_deg 0.699 r_mcangle_it 0.374 r_mcbond_it 0.214 r_mcbond_other 0.214 r_chiral_restr 0.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.639 r_dihedral_angle_4_deg 16.798 r_dihedral_angle_3_deg 12.439 r_dihedral_angle_1_deg 6.267 r_angle_refined_deg 0.998 r_angle_other_deg 0.699 r_mcangle_it 0.374 r_mcbond_it 0.214 r_mcbond_other 0.214 r_chiral_restr 0.061 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4523 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 18
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC phasing ARP model building Coot model building REFMAC refinement PDB_EXTRACT data extraction XSCALE data scaling