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Structure of the lactococcal phage 1358 receptor binding protein in complex with GlcNAc-1P
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4L92 PDB ENTRY 4L92
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.2 293 20% w/v polyethyleneglycol 1000, 100 mM sodium/potassium phosphate buffer, pH 6.2, 200 mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.39 71.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 165.91 α = 90 b = 165.91 β = 90 c = 165.91 γ = 90
Symmetry Space Group P 21 3
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 2014-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR
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 2.15 48 99.9 0.089 20.5 12.3 81936 49
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 2.15 2.21 99.9 0.81 2.43
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 MIR THROUGHOUT PDB ENTRY 4L92 2.15 47.89 38297 78636 3914 100 0.181 0.18 0.187 0.204 0.2072 RANDOM 45.25
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_long_range_B_other 9.341 r_long_range_B_refined 9.318 r_scangle_other 6.74 r_mcangle_other 5.458 r_mcangle_it 5.109 r_scbond_it 4.375 r_scbond_other 4.313 r_mcbond_it 3.444 r_mcbond_other 3.444 r_angle_refined_deg 1.893
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 9.341 r_long_range_B_refined 9.318 r_scangle_other 6.74 r_mcangle_other 5.458 r_mcangle_it 5.109 r_scbond_it 4.375 r_scbond_other 4.313 r_mcbond_it 3.444 r_mcbond_other 3.444 r_angle_refined_deg 1.893 r_angle_other_deg 1.093 r_chiral_restr 0.114 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.005 r_gen_planes_other 0.004 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6056 Nucleic Acid Atoms Solvent Atoms 502 Heterogen Atoms 38
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling