4IMO

Crystal structure of wild type human Lipocalin PGDS in complex with substrate analog U44069


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CZT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52770.1M potassium thiocyanate, 30% PEG MME 2000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
1.8934.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.24α = 90
b = 56.38β = 90
c = 72.92γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray198CCDADSC QUANTUM 3152011-09-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B10.97622NSRRCBL13B1

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
11.8836.491000.0780.0787.44.21273512735-323.5
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)RedundancyNumber Unique Reflections (All)
11.881.981000.3590.2742.84.21826

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 REPLACEMENTTHROUGHOUT2CZT1.8836.49-3120741207462099.980.191740.189110.24154RANDOM23.509
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]
0.16-0.710.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.653
r_dihedral_angle_4_deg13.963
r_dihedral_angle_3_deg11.994
r_dihedral_angle_1_deg6.316
r_angle_refined_deg1.508
r_angle_other_deg1.478
r_chiral_restr0.082
r_bond_refined_d0.011
r_bond_other_d0.007
r_gen_planes_refined0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.653
r_dihedral_angle_4_deg13.963
r_dihedral_angle_3_deg11.994
r_dihedral_angle_1_deg6.316
r_angle_refined_deg1.508
r_angle_other_deg1.478
r_chiral_restr0.082
r_bond_refined_d0.011
r_bond_other_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1215
Nucleic Acid Atoms
Solvent Atoms82
Heterogen Atoms56

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling