4IAX

Engineered human lipocalin 2 (CL31) in complex with Y-DTPA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DSZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6529317%(w/v) PEG3350, 0.4M potassium phosphate, pH 4.65, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3246.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.12α = 90
b = 60.12β = 90
c = 110.55γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2009-05-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.91841BESSY14.2

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
11.952.8299.90.06818.47.516702166922
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.921000.2450.2450.2630.0962.87.52388

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3DSZ1.952.822167021663584399.790.19720.19470.2446RANDOM22.3231
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]
0.30.3-0.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.445
r_dihedral_angle_4_deg24.024
r_dihedral_angle_3_deg14.655
r_dihedral_angle_1_deg6.244
r_scangle_it5.66
r_scbond_it3.567
r_mcangle_it2.112
r_angle_refined_deg1.909
r_mcbond_it1.216
r_chiral_restr0.158
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.445
r_dihedral_angle_4_deg24.024
r_dihedral_angle_3_deg14.655
r_dihedral_angle_1_deg6.244
r_scangle_it5.66
r_scbond_it3.567
r_mcangle_it2.112
r_angle_refined_deg1.909
r_mcbond_it1.216
r_chiral_restr0.158
r_bond_refined_d0.023
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1395
Nucleic Acid Atoms
Solvent Atoms116
Heterogen Atoms43

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection