2DDT

Crystal structure of sphingomyelinase from Bacillus cereus with magnesium ion

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	283	18% (w/v) PEG 8000, 0.2M magnesium sulfate, 0.1mM calcium chrolide, 0.1M MES, pH 6.5, VAPOR DIFFUSION, temperature 283K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.844	α = 81.87
b = 50.893	β = 81.84
c = 59.506	γ = 79.68

Symmetry
Space Group	P 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	RIGAKU JUPITER		2004-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1.000	SPring-8	BL26B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	90.8			48543	48543

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.9	93

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	1.8	49.69	48541	48541	2438	90.77	0.19478	0.19295	0.2	0.23024	0.24	RANDOM	19.288

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	0.4	0.76	-0.25	0.66	-0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.418
r_dihedral_angle_4_deg	16.469
r_dihedral_angle_3_deg	10.911
r_scangle_it	3.998
r_angle_other_deg	3.637
r_scbond_it	3.221
r_angle_refined_deg	2.161
r_mcangle_it	2.062
r_dihedral_angle_1_deg	2.014
r_mcbond_it	1.82
r_mcbond_other	0.392
r_symmetry_vdw_refined	0.293
r_chiral_restr	0.268
r_symmetry_vdw_other	0.263
r_nbd_other	0.246
r_nbd_refined	0.212
r_nbtor_refined	0.191
r_symmetry_hbond_refined	0.167
r_xyhbond_nbd_refined	0.122
r_nbtor_other	0.112
r_xyhbond_nbd_other	0.104
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_gen_planes_other	0.005
r_bond_other_d
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4570
Nucleic Acid Atoms
Solvent Atoms	534
Heterogen Atoms	38

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing