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Structure of laminin binding protein (Lmb) of Streptococcus agalactiae A bifunctional protein with adhesin and metal transporting activity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CX3 PDB ENTRY 3CX3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 293 30-35% (w/v) 30% PEG 2000 monoethyl ether, 0.1mM sodium citrate pH5.0, 5mM NiCl2 and 10% ethylene glycol, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.19 43.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.641 α = 90 b = 70.411 β = 96.14 c = 74.971 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 IMAGE PLATE MAR scanner 345 mm plate 2008-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
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 20 98.7 0.054 5.6 19066
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 0.274 1.4
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3CX3 2.5 20 19331 18322 875 94.8 0.234 0.234 0.2342 0.276 0.2764 RANDOM 55.6
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] 21.27 6.86 -7.86 -13.41
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22 c_angle_deg 1.4 c_improper_angle_d 0.94 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22 c_angle_deg 1.4 c_improper_angle_d 0.94 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4066 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 2
Software Software Software Name Purpose MAR345dtb data collection CNS refinement AUTOMAR data reduction CNS phasing