2HZQ

Crystal structure of human apolipoprotein D (ApoD) in complex with progesterone


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52931.1 M lithium sulfate, 0.1 M ammonium formate, 0.075 M Hepes/NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthew coefficientSolvent content
2.1643.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.206α = 90
b = 49.206β = 90
c = 144.126γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2006-03-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-11.00890ESRFID23-1

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
11.846.57598.70.070.076.611.317254170843
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)
1.81.995.30.3080.3082.311.22350

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTModel of uncomplexed ApoD1.830172541701386098.650.1890.1890.1870.226RANDOM22.551
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]
0.790.79-1.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.31
r_dihedral_angle_4_deg22.649
r_dihedral_angle_3_deg14.28
r_dihedral_angle_1_deg7.526
r_scangle_it4.265
r_scbond_it2.794
r_mcangle_it1.738
r_angle_refined_deg1.691
r_mcbond_it1.107
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.31
r_dihedral_angle_4_deg22.649
r_dihedral_angle_3_deg14.28
r_dihedral_angle_1_deg7.526
r_scangle_it4.265
r_scbond_it2.794
r_mcangle_it1.738
r_angle_refined_deg1.691
r_mcbond_it1.107
r_nbtor_refined0.312
r_symmetry_hbond_refined0.215
r_nbd_refined0.21
r_symmetry_vdw_refined0.193
r_xyhbond_nbd_refined0.135
r_chiral_restr0.104
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1327
Nucleic Acid Atoms
Solvent Atoms235
Heterogen Atoms23

Software

Software
Software NamePurpose
SCALAdata scaling
EPMRphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction
REFMACphasing