3M7O | pdb_00003m7o

Crystal structure of mouse MD-1 in complex with phosphatidylcholine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529322% (w/v) PEG-8000, 0.2 M Ammonium sulfate and MES pH 6.5,supplemented with 1/10 volume of 20% (w/v) benzamidine hydrochloride as a crystallization additive, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.299α = 90
b = 90.299β = 90
c = 86.714γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2702009-12-23MSINGLE WAVELENGTH
21x-ray100CCDADSC QUANTUM 210rMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3APhoton FactoryAR-NE3A
2SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12APhoton FactoryAR-NW12A

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
1,21.653098.40.06582260
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1,21.651.6886.90.5662.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSIRASTHROUGHOUT1.6529.96367139355198.130.196240.19460.1960.226590.2289RANDOM38.359
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]
0.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.484
r_dihedral_angle_4_deg16.255
r_dihedral_angle_3_deg13.639
r_scangle_it7.089
r_dihedral_angle_1_deg6.546
r_scbond_it4.481
r_mcangle_it3.372
r_mcbond_it2.015
r_angle_refined_deg1.405
r_chiral_restr0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.484
r_dihedral_angle_4_deg16.255
r_dihedral_angle_3_deg13.639
r_scangle_it7.089
r_dihedral_angle_1_deg6.546
r_scbond_it4.481
r_mcangle_it3.372
r_mcbond_it2.015
r_angle_refined_deg1.405
r_chiral_restr0.095
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4135
Nucleic Acid Atoms
Solvent Atoms444
Heterogen Atoms364

Software

Software
Software NamePurpose
HKL-2000data collection
autoSHARPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling