1Z17

Crystal structure analysis of periplasmic Leu/Ile/Val-binding protein with bound ligand isoleucine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Z16LIVBP-leu complex (closed form) without leucine and solvent, pdb entry 1Z16

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP527730 %MPD, 10mM CuSo4, 0.5 mM Lisoleucine and 50 mM Na-ccodylate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.5365.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.13α = 90
b = 99.13β = 90
c = 93.18γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMACSCIENCEgraphite monochromator1997-01-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.9650830.0510.05115.355571938888116.8
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)RedundancyNumber Unique Reflections (All)
11.962.1400.1840.1842.51.85412

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTLIVBP-leu complex (closed form) without leucine and solvent, pdb entry 1Z161.9621.883237531814158183.10.1830.205RANDOM19.7
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]
-0.361.91-0.360.71
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.1
c_scangle_it4.14
c_scbond_it2.92
c_mcangle_it2.36
c_mcbond_it1.61
c_angle_deg1.6
c_improper_angle_d1.12
c_bond_d0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2591
Nucleic Acid Atoms
Solvent Atoms351
Heterogen Atoms17

Software

Software
Software NamePurpose
CNSrefinement
MACSCIENCEdata reduction
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing