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Crystal structure of the lysosomal 66.3 kDa protein from mouse solved by S-SAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 12% (w/v) PEG 4000, 200mM NH4Ac, 100mM NaAc/HAc pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.39 63.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.804 α = 90 b = 89.672 β = 98.67 c = 64.954 γ = 90
Symmetry Space Group C 1 2 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 2008-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 1.9000 BESSY 14.2
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 50 98.9 0.083 48.813 23 33026 32641
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 2.49 97.5 0.373 10.2 21.2
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 SAD THROUGHOUT 2.4 32.11 30794 1620 98.08 0.15817 0.15603 0.1555 0.19804 0.1928 RANDOM 25.255
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] -0.5 -0.36 -0.48 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.31 r_dihedral_angle_4_deg 20.148 r_dihedral_angle_3_deg 16.265 r_dihedral_angle_1_deg 6.505 r_scangle_it 3.796 r_scbond_it 2.392 r_angle_refined_deg 1.436 r_mcangle_it 1.417 r_mcbond_it 0.701 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.31 r_dihedral_angle_4_deg 20.148 r_dihedral_angle_3_deg 16.265 r_dihedral_angle_1_deg 6.505 r_scangle_it 3.796 r_scbond_it 2.392 r_angle_refined_deg 1.436 r_mcangle_it 1.417 r_mcbond_it 0.701 r_nbtor_refined 0.304 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.168 r_xyhbond_nbd_refined 0.166 r_symmetry_hbond_refined 0.117 r_chiral_restr 0.1 r_metal_ion_refined 0.025 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other 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 4159 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 130
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHARP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling