1XX1 | pdb_00001xx1

Structural basis for ion-coordination and the catalytic mechanism of sphingomyelinases D

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.6	51.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.818	α = 90
b = 139.818	β = 90
c = 113.461	γ = 120

Symmetry
Space Group	P 65

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	MARRESEARCH		2004-08-09	M	SINGLE WAVELENGTH
2	1	100	IMAGE PLATE	MARRESEARCH	osmic mirrors	2004-08-20

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE D03B-MX1	1.427	LNLS	D03B-MX1
2	ROTATING ANODE	OTHER

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	1.75	30	99.5	0.057	22	20.5		125875

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)
	1.75	1.79	99.5		0.305	3.4	6.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	SIRAS	THROUGHOUT	1.75	30	119510	6315	99.51	0.198	0.18761	0.18566	0.1843	0.22465	0.2232	RANDOM	24.248

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]
0.04	0.02		0.04		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.728
r_dihedral_angle_3_deg	14.564
r_dihedral_angle_4_deg	14.26
r_dihedral_angle_1_deg	6.53
r_scangle_it	3.37
r_scbond_it	2.308
r_mcangle_it	1.634
r_angle_refined_deg	1.551
r_mcbond_it	0.955
r_nbtor_refined	0.328

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.728
r_dihedral_angle_3_deg	14.564
r_dihedral_angle_4_deg	14.26
r_dihedral_angle_1_deg	6.53
r_scangle_it	3.37
r_scbond_it	2.308
r_mcangle_it	1.634
r_angle_refined_deg	1.551
r_mcbond_it	0.955
r_nbtor_refined	0.328
r_nbd_refined	0.222
r_symmetry_hbond_refined	0.211
r_symmetry_vdw_refined	0.202
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.122
r_metal_ion_refined	0.066
r_bond_refined_d	0.013
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9076
Nucleic Acid Atoms
Solvent Atoms	1018
Heterogen Atoms	164

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling
SHELXS	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.