2DDS | pdb_00002dds

Crystal structure of sphingomyelinase from Bacillus cereus with cobalt 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 cobalt chloride, 0.1M MES, pH 6.5, VAPOR DIFFUSION, temperature 283K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.09	α = 112
b = 72.67	β = 90.05
c = 78.06	γ = 116.58

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	IMAGE PLATE	RIGAKU RAXIS VII		2004-08-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	1.77	35.8	91.1			103230	103230			15.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.77	1.83	83.6

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	19.67	98540	98540	9874	91.6	0.202	0.202	0.1987	0.232	0.2297	RANDOM	18.7

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]
-1.47	-0.3	0.15	-2.09	1.07	3.56

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	25
c_scangle_it	2.67
c_mcangle_it	1.86
c_scbond_it	1.85
c_angle_deg	1.3
c_mcbond_it	1.22
c_improper_angle_d	0.73
c_bond_d	0.005
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9320
Nucleic Acid Atoms
Solvent Atoms	1116
Heterogen Atoms	12

Software

Software
Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing