2E9M

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2E9L	PDB ENTRY 2E9L

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 galactose, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.4K

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.244	α = 90
b = 83.797	β = 90
c = 93.591	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	1.8	50	85.3	0.057	0.057	35.7	7.1	40776	40776

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)
	1.8	1.86	99.9		0.321	0.321	6.7	7.2	4816

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 2E9L	1.8	38.21	38042	38042	2006	81.88	0.20315	0.20315	0.20133	0.23642	RANDOM	21.962

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]
0.03			0.03		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.267
r_dihedral_angle_4_deg	19.075
r_dihedral_angle_3_deg	13.609
r_dihedral_angle_1_deg	6.131
r_scangle_it	2.172
r_scbond_it	1.381
r_angle_refined_deg	1.183
r_mcangle_it	0.899
r_mcbond_it	0.539
r_nbtor_refined	0.306
r_nbd_refined	0.195
r_symmetry_vdw_refined	0.158
r_symmetry_hbond_refined	0.15
r_xyhbond_nbd_refined	0.128
r_chiral_restr	0.085
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
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	3782
Nucleic Acid Atoms
Solvent Atoms	380
Heterogen Atoms	50

Software

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