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Orthorhombic Crystal Structure of Human Saposin C Dimer in Open Conformation
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 291 20 mM NaAcetate, 200 mM ammonium sulfate,
30% (v/v) pentaerythriol ethoxylate 15/4, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.85 56.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.008 α = 90 b = 88.904 β = 90 c = 93.465 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 IMAGE PLATE MAR scanner 345 mm plate Osmic MaxFlux 2003-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR571 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.45 32.2 99 0.055 17 2.89 8971 8971 2 3 76.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.45 2.54 99.8 0.46 2.1 898
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 2.45 28.5 2 7875 548 91.5 0.232 0.229 0.2228 0.29 0.2869 RANDOM 70.279
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] 0.41 -0.04 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.997 r_dihedral_angle_3_deg 18.866 r_dihedral_angle_1_deg 5.527 r_scangle_it 3.07 r_scbond_it 1.892 r_mcangle_it 1.354 r_angle_refined_deg 1.3 r_mcbond_it 0.787 r_nbtor_refined 0.298 r_nbd_refined 0.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.997 r_dihedral_angle_3_deg 18.866 r_dihedral_angle_1_deg 5.527 r_scangle_it 3.07 r_scbond_it 1.892 r_mcangle_it 1.354 r_angle_refined_deg 1.3 r_mcbond_it 0.787 r_nbtor_refined 0.298 r_nbd_refined 0.228 r_symmetry_vdw_refined 0.228 r_symmetry_hbond_refined 0.224 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1242 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection DENZO data reduction SCALEPACK data scaling