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Crystal structure of the Colicin I receptor Cir from E.coli in complex with receptor binding domain of Colicin Ia.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HDF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 294 9 G/L PROTEIN IN 0.02M TRIS PH7.5,
0.2M NACL, 0.05% LDAO, 0.45% C8E4, 3% HEPTANETRIOL MIXED AT
1:1 RATIO WITH 0.1M MES PH6.2, 10% GLYCEROL, 22% PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.84 56.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.633 α = 90 b = 130.494 β = 101.22 c = 56.261 γ = 90
Symmetry Space Group C 1 2 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 MARMOSAIC 300 mm CCD 2004-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
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 2.5 30 99.9 0.103 15.3 4.1 32311 32311
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 2.5 2.59 99.9 0.57 2.73 4 3632
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2HDF 2.5 15 29295 29295 1550 95.42 0.19097 0.19097 0.18781 0.24929 0.2517 RANDOM 44.618
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] -0.2 -0.61 -0.93 0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.317 r_dihedral_angle_4_deg 18.883 r_dihedral_angle_3_deg 16.01 r_scangle_it 8.066 r_dihedral_angle_1_deg 6.309 r_scbond_it 6.227 r_mcangle_it 3.613 r_mcbond_it 2.469 r_angle_refined_deg 1.303 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.317 r_dihedral_angle_4_deg 18.883 r_dihedral_angle_3_deg 16.01 r_scangle_it 8.066 r_dihedral_angle_1_deg 6.309 r_scbond_it 6.227 r_mcangle_it 3.613 r_mcbond_it 2.469 r_angle_refined_deg 1.303 r_nbtor_refined 0.3 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.164 r_xyhbond_nbd_refined 0.14 r_symmetry_hbond_refined 0.132 r_chiral_restr 0.093 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5510 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement PHASER phasing