1KXO

ENGINEERED LIPOCALIN DIGA16 : APO-FORM


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherThe structure of diga16 in presence of digoxigenin

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.62980.1-M Hepes, 10% Isopropanole, 19% PEG 4000, pH = 7.8, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.551.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.873α = 90
b = 63.476β = 92.02
c = 38.191γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATEMAR scanner 345 mm plate2001-11-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
11.848.2289.10.0414.22.31475414754-3
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)
1.81.8677.20.22.31.21260

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 SYNTHESISTHROUGHOUTThe structure of diga16 in presence of digoxigenin1.848.22146741467472689.450.212290.2090.289RANDOM28.316
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]
-0.210.1-2.682.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.968
r_scangle_it8.467
r_mcangle_it7.394
r_dihedral_angle_1_deg6.865
r_scbond_it6.409
r_mcbond_it5.672
r_angle_refined_deg2.684
r_angle_other_deg1.316
r_symmetry_vdw_refined0.266
r_nbd_refined0.249
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.968
r_scangle_it8.467
r_mcangle_it7.394
r_dihedral_angle_1_deg6.865
r_scbond_it6.409
r_mcbond_it5.672
r_angle_refined_deg2.684
r_angle_other_deg1.316
r_symmetry_vdw_refined0.266
r_nbd_refined0.249
r_symmetry_vdw_other0.245
r_nbd_other0.205
r_xyhbond_nbd_refined0.196
r_symmetry_hbond_refined0.187
r_chiral_restr0.162
r_bond_refined_d0.018
r_gen_planes_refined0.015
r_gen_planes_other0.01
r_bond_other_d0.001
r_nbtor_other
r_xyhbond_nbd_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 Atoms1320
Nucleic Acid Atoms
Solvent Atoms104
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing