3FBX

Crystal structure of the lysosomal 66.3 kDa protein from mouse solved by S-SAD


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP529312% (w/v) PEG 4000, 200mM NH4Ac, 100mM NaAc/HAc pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.3963.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 148.804α = 90
b = 89.672β = 98.67
c = 64.954γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2008-05-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.21.9000BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.45098.90.08348.813233302632641
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4997.50.37310.221.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.432.1130794162098.080.158170.156030.19804RANDOM25.255
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]
-0.5-0.36-0.480.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.31
r_dihedral_angle_4_deg20.148
r_dihedral_angle_3_deg16.265
r_dihedral_angle_1_deg6.505
r_scangle_it3.796
r_scbond_it2.392
r_angle_refined_deg1.436
r_mcangle_it1.417
r_mcbond_it0.701
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.31
r_dihedral_angle_4_deg20.148
r_dihedral_angle_3_deg16.265
r_dihedral_angle_1_deg6.505
r_scangle_it3.796
r_scbond_it2.392
r_angle_refined_deg1.436
r_mcangle_it1.417
r_mcbond_it0.701
r_nbtor_refined0.304
r_nbd_refined0.2
r_symmetry_vdw_refined0.168
r_xyhbond_nbd_refined0.166
r_symmetry_hbond_refined0.117
r_chiral_restr0.1
r_metal_ion_refined0.025
r_bond_refined_d0.013
r_gen_planes_refined0.005
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 AtomsNumber
Protein Atoms4159
Nucleic Acid Atoms
Solvent Atoms294
Heterogen Atoms130

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling