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Structure of the Monoclinic-3 (Monocln-3) Crystal Form of Human Apolipoprotein C1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ROP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 298 The crystals were grown by sitting drop vapor diffusion in Cryschem plates using 0.6 ml reservoirs of 16% to 18% 2-methyl-2,4-pentanediol (MPD) containing o.1 M sodium acetate and 0.25% octyl-beta-s-1-thioglucopyanoside. The drops were equal volumes, generally 6 ul each, of the reservoir and an 8 mg/ml solution of protein dissolved in .02 M ammonium bicarbonate.
Crystal Properties Matthews coefficient Solvent content 1.74 29.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.169 α = 90 b = 49.965 β = 105.1 c = 35.423 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 AREA DETECTOR SDMS 1992-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-D 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 30 70 0.131 0.131 0.15 0.071 0.987 4.6 2.6 5846
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.5 46.2 0.211 0.211 0.295 0.206 0.933 1.7 1.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1ROP 2.33 18.97 4148 226 78.37 0.20485 0.19879 0.31839 0.2902 RANDOM 21.243
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] 7.82 -10.95 9.24 -17.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.207 r_dihedral_angle_4_deg 19.832 r_dihedral_angle_3_deg 17.842 r_long_range_B_refined 5.491 r_long_range_B_other 5.332 r_dihedral_angle_1_deg 4.924 r_mcangle_it 2.246 r_mcangle_other 2.246 r_scangle_other 2.229 r_mcbond_it 1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.207 r_dihedral_angle_4_deg 19.832 r_dihedral_angle_3_deg 17.842 r_long_range_B_refined 5.491 r_long_range_B_other 5.332 r_dihedral_angle_1_deg 4.924 r_mcangle_it 2.246 r_mcangle_other 2.246 r_scangle_other 2.229 r_mcbond_it 1.38 r_mcbond_other 1.375 r_scbond_it 1.33 r_scbond_other 1.329 r_angle_refined_deg 1.093 r_angle_other_deg 0.643 r_chiral_restr 0.053 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 809 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction Aimless data scaling PHASER phasing