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Crystal structure analysis of periplasmic Leu/Ile/Val-binding protein with bound ligand isoleucine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z16 LIVBP-leu complex (closed form) without leucine and solvent, pdb entry 1Z16
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 277 30 %MPD, 10mM CuSo4, 0.5 mM Lisoleucine and 50 mM Na-ccodylate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.53 65.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.13 α = 90 b = 99.13 β = 90 c = 93.18 γ = 120
Symmetry Space Group P 31 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 IMAGE PLATE MACSCIENCE graphite monochromator 1997-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 1.96 50 83 0.051 0.051 15.3 5 55719 38888 1 1 6.8
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 1.96 2.1 40 0.184 0.184 2.5 1.8 5412
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-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT LIVBP-leu complex (closed form) without leucine and solvent, pdb entry 1Z16 1.96 21.88 32375 31814 1581 83.1 0.183 0.205 RANDOM 19.7
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] -0.36 1.91 -0.36 0.71
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.1 c_scangle_it 4.14 c_scbond_it 2.92 c_mcangle_it 2.36 c_mcbond_it 1.61 c_angle_deg 1.6 c_improper_angle_d 1.12 c_bond_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2591 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 17
Software Software Software Name Purpose CNS refinement MACSCIENCE data reduction DENZO data reduction SCALEPACK data scaling X-PLOR phasing