3NH9

Nucleotide Binding Domain of Human ABCB6 (ATP bound structure)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NH6PDB entry 3NH6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52980.1M MES pH 6.5, 40% (v/v) PEG400, 30mM ATP, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9536.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.152α = 90
b = 65.626β = 90
c = 69.522γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2009-09-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.124.5297.70.0715.83.71581015449-332.859
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1590.42.93.31130

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 REPLACEMENTTHROUGHOUTPDB entry 3NH62.124.52-315810154497731000.1790.1750.248RANDOM30.314
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]
-1.180.520.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.448
r_dihedral_angle_4_deg18.597
r_dihedral_angle_3_deg17.077
r_dihedral_angle_1_deg6.102
r_scangle_it4.396
r_scbond_it2.774
r_angle_refined_deg1.744
r_mcangle_it1.551
r_mcbond_it0.87
r_chiral_restr0.113
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.448
r_dihedral_angle_4_deg18.597
r_dihedral_angle_3_deg17.077
r_dihedral_angle_1_deg6.102
r_scangle_it4.396
r_scbond_it2.774
r_angle_refined_deg1.744
r_mcangle_it1.551
r_mcbond_it0.87
r_chiral_restr0.113
r_bond_refined_d0.019
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2089
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms39

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
XDSdata reduction