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X-ray structure of the bacteriophage phiKZ lytic transglycosylase, gp144, in complex with chitotetraose, (NAG)4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BKH Structure of the phiKZ gp144 (PDB code 3BKH)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 1.2% (v/v) polyethylene glycol 400, 60 mM HEPES sodium, pH 7.5. Presence of DTT (5mM) in the protein solution was important for crystallization, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.39 63.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.322 α = 90 b = 62.322 β = 90 c = 182.643 γ = 120
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++ 2007-05-15 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 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 2.6 40.39 99.7 0.077 45.6 8.6 12316 12279 1 47.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 99 0.255 14 8
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 Structure of the phiKZ gp144 (PDB code 3BKH) 2.6 40.39 12279 1262 99.7 0.227 0.227 0.2391 0.272 0.286 RANDOM 48.3
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] -1.99 -1.99 3.99
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.7 c_angle_deg 1.3 c_improper_angle_d 0.88 c_bond_d 0.007 c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2095 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 63
Software Software Software Name Purpose HKL-2000 data collection CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing