2E9L

Crystal Structure of human Cytosolic Neutral beta-Glycosylceramidase (Klotho-related Prote:KLrP) complex with Glucose and fatty acids

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293.4	27.5% PEG3350, 0.1M Tris-HCl buffer, pH 8.5, 0.2M magnesium chloride, 5% glycerol, 0.5M glucose , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.4K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.035	α = 90
b = 83.976	β = 90
c = 94.882	γ = 90

Symmetry
Space Group	P 21 21 21

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	RIGAKU JUPITER 210		2006-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0	SPring-8	BL38B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.6	50	89.5	0.133	0.133	44.7	7.1	446923	446923

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.66	95.5		0.421	0.421	5.7	7.1	6633

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1WCG	1.6	21.29	59292	59292	3201	88.86	0.18949	0.18949	0.18777	0.2214	RANDOM	17.449

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.672
r_dihedral_angle_4_deg	18.216
r_dihedral_angle_3_deg	13.134
r_dihedral_angle_1_deg	10.947
r_scangle_it	2.055
r_scbond_it	1.357
r_angle_refined_deg	1.228
r_mcangle_it	0.818
r_mcbond_it	0.609
r_nbtor_refined	0.311
r_symmetry_vdw_refined	0.24
r_nbd_refined	0.198
r_xyhbond_nbd_refined	0.11
r_symmetry_hbond_refined	0.093
r_chiral_restr	0.088
r_bond_refined_d	0.008
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_refined
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	3778
Nucleic Acid Atoms
Solvent Atoms	450
Heterogen Atoms	86

Software

Software
Software Name	Purpose
REFMAC	refinement
BSS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing