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Structure of the Monoclinic-1 (Monocl-1) 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, SITTING DROP 8 298 Crystallized in Cryschem sitting drop plates with reservoirs of 16%-18% 2-methyl-2,4-pentanediol (MPD), 0.1 M sodium acetate and 0.25% octyl-beta-s-1-thioglucopyanoside. The drops were composed of equal amounts of 8 mg/ml protein in 0.02 ammonium bicarbonate and reservoir.
Crystal Properties Matthews coefficient Solvent content 1.87 34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.541 α = 90 b = 46.739 β = 95.16 c = 33.88 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 1992-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.8 35 85.2 0.094 0.094 0.114 0.055 0.993 6.7 7.2 7315
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 1.8 1.95 76 0.457 0.457 0.721 0.315 0.64 3.2 4.5
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 1ROP 1.8 33 6965 353 84.97 0.22426 0.22139 0.2288 0.27626 0.2759 RANDOM 32.597
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] 1.91 -0.49 -0.02 -1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.618 r_dihedral_angle_4_deg 18.166 r_dihedral_angle_3_deg 16.124 r_long_range_B_refined 10.757 r_long_range_B_other 10.754 r_scangle_other 8.977 r_scbond_it 5.896 r_scbond_other 5.89 r_mcangle_other 4.973 r_mcangle_it 4.971
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.618 r_dihedral_angle_4_deg 18.166 r_dihedral_angle_3_deg 16.124 r_long_range_B_refined 10.757 r_long_range_B_other 10.754 r_scangle_other 8.977 r_scbond_it 5.896 r_scbond_other 5.89 r_mcangle_other 4.973 r_mcangle_it 4.971 r_dihedral_angle_1_deg 3.956 r_mcbond_it 3.539 r_mcbond_other 3.517 r_angle_refined_deg 1.049 r_angle_other_deg 0.608 r_chiral_restr 0.055 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 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 859 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement UCSD-system data reduction Aimless data scaling PHASER phasing