1LKE

ENGINEERED LIPOCALIN DIGA16 IN COMPLEX WITH DIGOXIGENIN


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BBPpdb entry 1BBP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82980.1-M HEPES, 10% ISOPROPANOL, 19% PEG 4000, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.551.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.052α = 90
b = 63.988β = 91.53
c = 39.452γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATEMAR scanner 345 mm plateOSMIC MIRRORS2001-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU300

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.99996.70.06222.21429414294-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.91.9796.10.2261.91411

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-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTpdb entry 1BBP1.948.8143301359973196.90.188080.184950.24753RANDOM33.566
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]
-0.020.14-1.611.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg16.879
r_scangle_it8.136
r_mcangle_it6.837
r_scbond_it5.709
r_dihedral_angle_1_deg5.123
r_mcbond_it4.556
r_angle_refined_deg1.541
r_symmetry_vdw_refined0.314
r_nbd_refined0.209
r_xyhbond_nbd_refined0.179
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg16.879
r_scangle_it8.136
r_mcangle_it6.837
r_scbond_it5.709
r_dihedral_angle_1_deg5.123
r_mcbond_it4.556
r_angle_refined_deg1.541
r_symmetry_vdw_refined0.314
r_nbd_refined0.209
r_xyhbond_nbd_refined0.179
r_chiral_restr0.152
r_symmetry_hbond_refined0.135
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1245
Nucleic Acid Atoms
Solvent Atoms58
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing