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Crystal structure of chicken MD-1 complexed with lipid IVa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MTX PDB ID, 3MTX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 296 17% PEG 2000, 100mM MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.29 46.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.465 α = 90 b = 78.15 β = 90 c = 101.236 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 315 KOHZU: Double Crystal Si(111) 2008-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0333 ALS 8.2.2
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 2.4 20 98.2 0.044 4.4 12503
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) 2.4 2.49 0.371 6.6 4.3 1213
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 ID, 3MTX 2.4 20 11843 612 97.6 0.23388 0.23213 0.2434 0.26703 0.271 RANDOM 32.058
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] -1.74 3.89 -2.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.897 r_dihedral_angle_3_deg 20.323 r_dihedral_angle_4_deg 18.564 r_dihedral_angle_1_deg 10.911 r_scangle_it 5.75 r_scbond_it 4.087 r_mcangle_it 2.472 r_angle_refined_deg 1.686 r_mcbond_it 1.543 r_angle_other_deg 0.992
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.897 r_dihedral_angle_3_deg 20.323 r_dihedral_angle_4_deg 18.564 r_dihedral_angle_1_deg 10.911 r_scangle_it 5.75 r_scbond_it 4.087 r_mcangle_it 2.472 r_angle_refined_deg 1.686 r_mcbond_it 1.543 r_angle_other_deg 0.992 r_mcbond_other 0.506 r_chiral_restr 0.112 r_bond_refined_d 0.017 r_gen_planes_refined 0.017 r_gen_planes_other 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2181 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 204
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling