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Crystal structure of human apoM in complex with glycerol 1- myristic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WEW PDB ENTRY 2WEW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.2 ABOUT 1-2 MICROL OF PROTEIN (10-16 MG/ML IN 20 MM TRIS-HCL, PH 7.2) WERE MIXED WITH 1-2 MICROL OF 30 % PEG1500 (W/V, IN DEIONISED WATER) AND EQUILIBRATED AGAINST 700 MICROL OF RESERVOIR SOLUTION CONTAINING 30 % PEG1500.
Crystal Properties Matthews coefficient Solvent content 2.39 47.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.82 α = 90 b = 49.82 β = 90 c = 145.48 γ = 90
Symmetry Space Group P 43 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 RAYONIX M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 20 99.7 0.05 23.53 8.41 13097 3 42.3
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 2.12 99.7 0.54 4.11 8.49
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 ENTRY 2WEW 2 19 12429 654 100 0.21075 0.20831 0.21 0.25708 0.2486 RANDOM 19.847
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] -1.8 -1.8 3.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.487 r_dihedral_angle_4_deg 19.787 r_dihedral_angle_3_deg 18.381 r_dihedral_angle_1_deg 7.02 r_scangle_it 3.614 r_scbond_it 2.606 r_angle_refined_deg 1.8 r_mcangle_it 1.527 r_mcbond_it 1.047 r_symmetry_hbond_refined 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.487 r_dihedral_angle_4_deg 19.787 r_dihedral_angle_3_deg 18.381 r_dihedral_angle_1_deg 7.02 r_scangle_it 3.614 r_scbond_it 2.606 r_angle_refined_deg 1.8 r_mcangle_it 1.527 r_mcbond_it 1.047 r_symmetry_hbond_refined 0.33 r_nbtor_refined 0.306 r_nbd_refined 0.233 r_symmetry_vdw_refined 0.214 r_xyhbond_nbd_refined 0.185 r_chiral_restr 0.124 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1253 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing