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Crystal Structure of Human Saposin D (triclinic)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SAPOSIN D P212121
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 PEG 4K, ZINC SULFATE, SODIUM ACETATE BUFFER, PH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.84 56.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.66 α = 89.9 b = 41.12 β = 81.2 c = 65.45 γ = 71.4
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 BRUKER SMART 6000 2007-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
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 65 92.6 0.056 20.4 3.52 24429
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) 2 2.05 91.2 0.1406 6.73 1.4
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 SAPOSIN D P212121 2 64.55 24429 1308 96 0.19756 0.19514 0.1952 0.24217 0.2397 RANDOM 21.496
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] 0.83 0.25 -0.01 -0.04 -0.54 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.345 r_dihedral_angle_4_deg 14.874 r_dihedral_angle_3_deg 13.362 r_dihedral_angle_1_deg 5.733 r_scangle_it 3.014 r_scbond_it 1.885 r_angle_refined_deg 1.399 r_mcangle_it 1.375 r_mcbond_it 0.845 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.345 r_dihedral_angle_4_deg 14.874 r_dihedral_angle_3_deg 13.362 r_dihedral_angle_1_deg 5.733 r_scangle_it 3.014 r_scbond_it 1.885 r_angle_refined_deg 1.399 r_mcangle_it 1.375 r_mcbond_it 0.845 r_nbtor_refined 0.299 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.2 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.1 r_symmetry_hbond_refined 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2477 Nucleic Acid Atoms Solvent Atoms 314 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement PROTEUM PLUS data collection PROTEUM PLUS data reduction PROTEUM PLUS data scaling