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Crystal structure analysis of periplasmic Leu/Ile/Val-binding protein with bound valine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z16 liv-leu complex without bound leu and solvent, pdb entry 1Z16
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 25% (v/v) PEG-400, 0.1 M succinic acid, 50 mM CdSo4 and 50 mM Na-cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.42 α = 90 b = 70.34 β = 90 c = 82.9 γ = 90
Symmetry Space Group P 21 21 21
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 1998-04-05 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 2.1 50 92 0.129 0.129 5.4 3 45340 18896 1 1 0.5
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 2.1 2.2 85 0.242 0.242 2.2 2 18896
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 liv-leu complex without bound leu and solvent, pdb entry 1Z16 2.1 29.21 18896 18896 919 92 0.216 0.262 RANDOM 13.3
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] 1.85 -3.83 1.97
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.5 c_angle_deg 1.6 c_improper_angle_d 1.04 c_bond_d 0.011 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 23.5 c_angle_deg 1.6 c_improper_angle_d 1.04 c_bond_d 0.011 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 2591 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 11
Software Software Software Name Purpose CNS refinement MACSCIENCE data reduction DENZO data reduction SCALEPACK data scaling EPMR phasing GEHLHAAR) phasing