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Crystal structure of a chimeric receptor binding protein from lactococcal phages subspecies TP901-1 and p2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BSD PDB ENTRY 2BSD, 2F0C experimental model PDB 2F0C PDB ENTRY 2BSD, 2F0C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.1M Sodium Cacodylate, 12% MPEG2000, pH5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.95 58.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.833 α = 90 b = 85.833 β = 90 c = 85.833 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 CCD ADSC QUANTUM 210 toroidal mirror 2007-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9340 ESRF ID14-1
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 3.35 85.75 100 0.245 0.245 15.9 19.9 3206 3206 20.5
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 3.35 3.53 100 0.509 0.509 6.6 20.5 450
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 (All) 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 PDB ENTRY 2BSD, 2F0C 3.35 60.69 2744 2744 450 99.97 0.22853 0.22853 0.22108 0.2088 0.27437 0.2764 RANDOM 27.928
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_dihedral_angle_2_deg 40.17 r_dihedral_angle_4_deg 22.051 r_dihedral_angle_3_deg 19.889 r_dihedral_angle_1_deg 5.469 r_scangle_it 1.914 r_angle_refined_deg 1.307 r_scbond_it 1.177 r_mcangle_it 0.784 r_mcbond_it 0.624 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.17 r_dihedral_angle_4_deg 22.051 r_dihedral_angle_3_deg 19.889 r_dihedral_angle_1_deg 5.469 r_scangle_it 1.914 r_angle_refined_deg 1.307 r_scbond_it 1.177 r_mcangle_it 0.784 r_mcbond_it 0.624 r_nbtor_refined 0.312 r_nbd_refined 0.268 r_symmetry_vdw_refined 0.255 r_xyhbond_nbd_refined 0.192 r_symmetry_hbond_refined 0.178 r_chiral_restr 0.096 r_bond_refined_d 0.013 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1137 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling BALBES phasing