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Crystal structure of saposin A in complex with lauryldimethylamine-N-oxide (LDAO)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 300 1.6 M trisodium citrate, pH 6.5, VAPOR DIFFUSION, temperature 300K
Crystal Properties Matthews coefficient Solvent content 3.12 60.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.794 α = 90 b = 39.794 β = 90 c = 247.284 γ = 120
Symmetry Space Group P 61 2 2
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 315 2009-07-25 M SINGLE WAVELENGTH 2 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2009-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.009 APS 19-ID 2 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 2.292
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 1.9 34.5 98.7 0.051 44.9 9.1 10065 9934 31.3
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 1.9 1.93 98.1 0.443 3.2 5.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD THROUGHOUT 1.9 10 9889 9889 478 99.3 0.232 0.23 0.2436 0.28 0.2857 RANDOM 41.21
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] 1.05 0.52 1.05 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.434 r_dihedral_angle_3_deg 14.674 r_dihedral_angle_4_deg 10.914 r_dihedral_angle_1_deg 4.576 r_scangle_it 4.55 r_scbond_it 2.825 r_mcangle_it 2.19 r_angle_refined_deg 1.9 r_mcbond_it 1.196 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.434 r_dihedral_angle_3_deg 14.674 r_dihedral_angle_4_deg 10.914 r_dihedral_angle_1_deg 4.576 r_scangle_it 4.55 r_scbond_it 2.825 r_mcangle_it 2.19 r_angle_refined_deg 1.9 r_mcbond_it 1.196 r_chiral_restr 0.112 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 606 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 320
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling SHELXS phasing