3ROZ

Crystal Structure of Mouse Apolipoprotein A-I Binding Protein in Complex with Nicotinamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2O8NPDB ENTRY 2O8N

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62930.1 M SODIUM ACETATE, 1.5 M AMMONIUM SULFATE, PH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.0259.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.115α = 90
b = 125.115β = 90
c = 119.801γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rMIRRORS2009-06-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97918APS19-BM

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
12.85084.40.0860.08639.1196.85292852928-389.9
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)
12.82.8595.40.5680.5682.7776.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2O8N2.850749436082.740.210.2080.243RANDOM151.936
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]
-6.85-3.42-6.8510.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.338
r_dihedral_angle_3_deg17.655
r_dihedral_angle_4_deg10.253
r_dihedral_angle_1_deg7.151
r_scangle_it4.979
r_mcangle_it4.469
r_angle_other_deg4.007
r_scbond_it3.07
r_mcbond_it2.588
r_angle_refined_deg1.457
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.338
r_dihedral_angle_3_deg17.655
r_dihedral_angle_4_deg10.253
r_dihedral_angle_1_deg7.151
r_scangle_it4.979
r_mcangle_it4.469
r_angle_other_deg4.007
r_scbond_it3.07
r_mcbond_it2.588
r_angle_refined_deg1.457
r_chiral_restr0.073
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_gen_planes_other0.004
r_mcbond_other0.003
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1808
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing