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Crystal structure of a cleaved form 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
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.1 293 0.1M Imidazole-malate, 17% PEG4000, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.75991 30.110064
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.168 α = 90 b = 43.682 β = 101.63 c = 78.946 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 210 tiroidal 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 1.65 39.01 98.3 0.166 0.166 7.7 3 48882 48882 23.4
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 1.65 1.74 99.9 0.394 0.394 2.3 3.1 6921
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 MIR THROUGHOUT PDB entry 2bsd 1.65 30 44350 44350 1164 98.26 0.16505 0.16505 0.16411 0.1722 0.20149 0.2021 RANDOM 15.527
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] 0.03 -0.73 -0.4 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.477 r_dihedral_angle_4_deg 21.689 r_dihedral_angle_3_deg 10.95 r_dihedral_angle_1_deg 6.534 r_scangle_it 4.181 r_scbond_it 3.093 r_angle_refined_deg 1.686 r_mcbond_it 1.667 r_mcangle_it 1.659 r_angle_other_deg 0.862
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.477 r_dihedral_angle_4_deg 21.689 r_dihedral_angle_3_deg 10.95 r_dihedral_angle_1_deg 6.534 r_scangle_it 4.181 r_scbond_it 3.093 r_angle_refined_deg 1.686 r_mcbond_it 1.667 r_mcangle_it 1.659 r_angle_other_deg 0.862 r_mcbond_other 0.327 r_nbd_other 0.214 r_symmetry_vdw_other 0.214 r_symmetry_vdw_refined 0.205 r_nbd_refined 0.19 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.15 r_symmetry_hbond_refined 0.146 r_chiral_restr 0.101 r_nbtor_other 0.086 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3080 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling PHASER phasing