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Crystal structure of human MD-2 in complex with lipid IVa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E56 PDB ENTRY 2E56
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 277 15% PEG3350, 40mM Na-citrate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal Properties Matthews coefficient Solvent content 2.33 47.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.795 α = 90 b = 52.795 β = 90 c = 110.889 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU JUPITER 210 2006-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0000 SPring-8 BL38B1
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 2.2 27.72 90.7 0.1 9.6 11.2 7629 25.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2E56 2.21 27.72 2.5 6291 297 78.88 0.20842 0.20583 0.1986 0.26326 0.2613 RANDOM 37.455
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] 1.08 1.08 -2.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.862 r_dihedral_angle_3_deg 16.278 r_dihedral_angle_4_deg 8.002 r_dihedral_angle_1_deg 6.597 r_scangle_it 6.181 r_mcangle_it 6.072 r_scbond_it 4.389 r_mcbond_it 4.014 r_angle_refined_deg 1.495 r_nbtor_refined 0.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.862 r_dihedral_angle_3_deg 16.278 r_dihedral_angle_4_deg 8.002 r_dihedral_angle_1_deg 6.597 r_scangle_it 6.181 r_mcangle_it 6.072 r_scbond_it 4.389 r_mcbond_it 4.014 r_angle_refined_deg 1.495 r_nbtor_refined 0.344 r_nbd_refined 0.259 r_symmetry_vdw_refined 0.255 r_xyhbond_nbd_refined 0.233 r_symmetry_hbond_refined 0.218 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1162 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 123
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing