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Crystal Structure of Mouse Apolipoprotein M
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 5.6 0.1 M NA CITRATE PH 5.6, 20% V/V 2-PROPANOL, 20% W/V PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.28 46.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.93 α = 90 b = 53.93 β = 90 c = 207.48 γ = 120
Symmetry Space Group P 65 2 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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BESSY
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 2.5 20 99.7 0.18 10.84 7.7 6802 2 26.489
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 2.5 2.65 99.9 0.58 3.56 8.08
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 2.5 19.94 6450 340 100 0.19033 0.18731 0.1875 0.2473 0.2504 RANDOM 11.554
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] 0.91 0.46 0.91 -1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.819 r_dihedral_angle_4_deg 20.219 r_dihedral_angle_3_deg 19.905 r_dihedral_angle_1_deg 6.706 r_scangle_it 2.989 r_scbond_it 1.742 r_angle_refined_deg 1.607 r_mcangle_it 1.104 r_mcbond_it 0.553 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.819 r_dihedral_angle_4_deg 20.219 r_dihedral_angle_3_deg 19.905 r_dihedral_angle_1_deg 6.706 r_scangle_it 2.989 r_scbond_it 1.742 r_angle_refined_deg 1.607 r_mcangle_it 1.104 r_mcbond_it 0.553 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.247 r_nbd_refined 0.225 r_symmetry_hbond_refined 0.209 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.107 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 1163 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing