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Crystal Structure of Human Saposin D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R0R pdb entry 2r0r
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 2.63 53.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.154 α = 89.96 b = 41.088 β = 80.84 c = 65.929 γ = 71.49
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate mirrors 2002-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER 1.54179
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 2.1 30 94.5 0.051 22 21734 39
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) 1 2.1 2.18 91.7 0.185 2109
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 THROUGHOUT pdb entry 2r0r 2.1 21.67 21733 1100 94.58 0.214 0.211 0.2086 0.274 0.268 RANDOM 29.617
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] 0.04 0.02 -0.02 0.02 -0.09 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.571 r_dihedral_angle_4_deg 21.067 r_dihedral_angle_3_deg 13.964 r_dihedral_angle_1_deg 5.441 r_scangle_it 1.79 r_angle_refined_deg 1.247 r_scbond_it 1.13 r_mcangle_it 0.919 r_mcbond_it 0.551 r_nbtor_refined 0.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.571 r_dihedral_angle_4_deg 21.067 r_dihedral_angle_3_deg 13.964 r_dihedral_angle_1_deg 5.441 r_scangle_it 1.79 r_angle_refined_deg 1.247 r_scbond_it 1.13 r_mcangle_it 0.919 r_mcbond_it 0.551 r_nbtor_refined 0.292 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.135 r_symmetry_vdw_refined 0.127 r_symmetry_hbond_refined 0.123 r_chiral_restr 0.087 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2450 Nucleic Acid Atoms Solvent Atoms 381 Heterogen Atoms 27
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection AMoRE phasing