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Crystal Structure of Human Saposin D variant SapD K9E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.9 291 100 mM BisTris, 2.3 M ammonium sulfate, 100 mM urea, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.66 53.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.434 α = 90 b = 66.029 β = 114.83 c = 42.467 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 100 CCD MAR CCD 165 mm mirrors 2005-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.954 BESSY 14.1
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 2.5 30 94.6 0.075 14.7 3.2 6704 43.8
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) 2.5 2.59 71.6 0.118 486
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.5 25.07 6693 313 94.6 0.214 0.21 0.2076 0.287 0.2793 RANDOM 27.726
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] -1.44 0.69 0.07 1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.878 r_dihedral_angle_3_deg 17.182 r_dihedral_angle_4_deg 6.7 r_dihedral_angle_1_deg 5.101 r_scangle_it 1.474 r_angle_refined_deg 1.197 r_scbond_it 0.912 r_mcangle_it 0.791 r_mcbond_it 0.458 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.878 r_dihedral_angle_3_deg 17.182 r_dihedral_angle_4_deg 6.7 r_dihedral_angle_1_deg 5.101 r_scangle_it 1.474 r_angle_refined_deg 1.197 r_scbond_it 0.912 r_mcangle_it 0.791 r_mcbond_it 0.458 r_nbtor_refined 0.301 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.178 r_symmetry_hbond_refined 0.122 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1220 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 5
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection