3FBX | pdb_00003fbx

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

X-RAY DIFFRACTION

---

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	0.16	0.19804	0.19	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
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