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Crystal structure of human apolipoprotein D (ApoD)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 1.1 M lithium sulfate, 0.1 M ammonium formate, 0.075 M Hepes/NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.15 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.247 α = 90 b = 49.247 β = 90 c = 143.486 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 ADSC QUANTUM 4 mirrors 2005-07-11 M MAD 2 1 3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.97940,0.97969,0.96863 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.8 46.58 99.1 0.067 0.067 6.4 15 17219 17002 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.9 98.7 0.285 0.285 2.2 14.7 2437
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MAD THROUGHOUT 1.8 30 17219 16987 864 98.7 0.205 0.205 0.202 0.2028 0.25 0.2522 RANDOM 22.818
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] 0.78 0.78 -1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.702 r_dihedral_angle_4_deg 20.116 r_dihedral_angle_3_deg 12.398 r_dihedral_angle_1_deg 6.13 r_scangle_it 4.474 r_scbond_it 2.987 r_mcangle_it 1.806 r_angle_refined_deg 1.431 r_mcbond_it 1.185 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.702 r_dihedral_angle_4_deg 20.116 r_dihedral_angle_3_deg 12.398 r_dihedral_angle_1_deg 6.13 r_scangle_it 4.474 r_scbond_it 2.987 r_mcangle_it 1.806 r_angle_refined_deg 1.431 r_mcbond_it 1.185 r_nbtor_refined 0.308 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.209 r_symmetry_hbond_refined 0.167 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.104 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1283 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling SHARP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction