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Crystal Structure of Human Saposin C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M12 PDB entry 1M12
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 PEG400, Calcium Chloride, Sodium Hepes, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.3 46.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.204 α = 90 b = 53.204 β = 90 c = 52.46 γ = 120
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 2003-09-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F2 0.9794 CHESS F2
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 2.4 26 96.2 0.06 15.2 3896 3896 -3
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 2.4 2.48 74.9 0.25
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1M12 2.4 20 2812 2812 465 97.76 0.22 0.22136 0.21083 0.2113 0.28257 0.2822 RANDOM 75.575
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] 1.69 0.85 1.69 -2.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 49.644 r_dihedral_angle_3_deg 18.081 r_dihedral_angle_1_deg 7.751 r_scangle_it 3.249 r_scbond_it 2.105 r_angle_refined_deg 1.729 r_mcangle_it 1.338 r_mcbond_it 0.909 r_symmetry_vdw_refined 0.344 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 49.644 r_dihedral_angle_3_deg 18.081 r_dihedral_angle_1_deg 7.751 r_scangle_it 3.249 r_scbond_it 2.105 r_angle_refined_deg 1.729 r_mcangle_it 1.338 r_mcbond_it 0.909 r_symmetry_vdw_refined 0.344 r_nbtor_refined 0.304 r_nbd_refined 0.25 r_xyhbond_nbd_refined 0.224 r_symmetry_hbond_refined 0.136 r_chiral_restr 0.114 r_bond_refined_d 0.019 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 609 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing