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Crystal structure of mouse MD-1 in complex with phosphatidylcholine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 22% (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 = 90.299 α = 90 b = 90.299 β = 90 c = 86.714 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 270 2009-12-23 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 210r M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A Photon Factory AR-NE3A 2 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1,2 1.65 30 98.4 0.065 82260
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 1.65 1.68 86.9 0.566 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION SIRAS THROUGHOUT 1.65 29.96 3 67139 3551 98.13 0.19624 0.1946 0.196 0.22659 0.2289 RANDOM 38.359
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.484 r_dihedral_angle_4_deg 16.255 r_dihedral_angle_3_deg 13.639 r_scangle_it 7.089 r_dihedral_angle_1_deg 6.546 r_scbond_it 4.481 r_mcangle_it 3.372 r_mcbond_it 2.015 r_angle_refined_deg 1.405 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.484 r_dihedral_angle_4_deg 16.255 r_dihedral_angle_3_deg 13.639 r_scangle_it 7.089 r_dihedral_angle_1_deg 6.546 r_scbond_it 4.481 r_mcangle_it 3.372 r_mcbond_it 2.015 r_angle_refined_deg 1.405 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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 Atoms Number Protein Atoms 4135 Nucleic Acid Atoms Solvent Atoms 444 Heterogen Atoms 364
Software Software Software Name Purpose HKL-2000 data collection autoSHARP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling