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Crystal and cryoEM structural studies of a cell wall degrading enzyme in the bacteriophage phi29 tail
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 20% PEG4000, 100mM Tris-HCl, 10% glycerol, 10mM NAG4, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.05 40.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.876 α = 90 b = 69.35 β = 90 c = 70.728 γ = 90
Symmetry Space Group P 21 21 21
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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.77 22.1 97.4 0.035 3.5 35.6 14874
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.83 89.6 0.171 17.1 9.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FOURIER SYNTHESIS THROUGHOUT 1.77 22.05 13365 1509 98.69 0.19934 0.19482 0.2033 0.23811 0.2484 RANDOM 29.084
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] 0.08 -0.52 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.062 r_dihedral_angle_4_deg 20.166 r_dihedral_angle_3_deg 12.65 r_dihedral_angle_1_deg 6.313 r_scangle_it 2.44 r_scbond_it 1.898 r_angle_refined_deg 1.544 r_mcangle_it 1.117 r_mcbond_it 0.782 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.062 r_dihedral_angle_4_deg 20.166 r_dihedral_angle_3_deg 12.65 r_dihedral_angle_1_deg 6.313 r_scangle_it 2.44 r_scbond_it 1.898 r_angle_refined_deg 1.544 r_mcangle_it 1.117 r_mcbond_it 0.782 r_nbtor_refined 0.313 r_nbd_refined 0.237 r_symmetry_hbond_refined 0.206 r_symmetry_vdw_refined 0.2 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.095 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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 1296 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling