2UYR

Crystal structure of Bacillus cereus sphingomyelinase mutant :N57A

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		0.1 M CALCIUM ACETATE 0.2 M SODIUM CACODYLATE (PH7.5) 18% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.09	α = 90
b = 63.927	β = 90
c = 101.69	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		RIGAKU IMAGING PLATE	MIRRORS	2006-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E

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	48.44	98.7	0.15	4.9	11.2		14493		1

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	96.5		0.33

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2DDT	2.4	54.15	13721	724	98.6	0.184	0.182	0.18	0.235	RANDOM	27.52

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]
0.77			-0.08		-0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.539
r_dihedral_angle_4_deg	19.305
r_dihedral_angle_3_deg	17.718
r_dihedral_angle_1_deg	7.175
r_scangle_it	4.141
r_scbond_it	2.71
r_mcangle_it	2.046
r_angle_refined_deg	1.631
r_mcbond_it	1.139
r_angle_other_deg	0.761
r_symmetry_hbond_refined	0.356
r_nbtor_refined	0.306
r_nbtor_other	0.274
r_nbd_other	0.228
r_symmetry_vdw_refined	0.224
r_nbd_refined	0.207
r_xyhbond_nbd_refined	0.145
r_chiral_restr	0.121
r_mcbond_other	0.106
r_bond_other_d	0.059
r_metal_ion_refined	0.023
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_gen_planes_other	0.006
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2361
Nucleic Acid Atoms
Solvent Atoms	89
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CCP4I	phasing