3H4X

Structure of a Ca+2 dependent Phosphatidylinositol-specific phospholipase C (PI-PLC) Enzyme from Streptomyces antibioticus

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	277	21% PEG 10000, 85mM sodium acetate pH 4.6, 170mM ammonium acetate, 9% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.968	α = 90
b = 154.819	β = 90
c = 41.324	γ = 90

Symmetry
Space Group	P 21 21 2

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	MARMOSAIC 325 mm CCD		2008-01-01	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.82653	SSRL	BL9-2

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	1.23	51.99	99.92	0.049	8.2141	7.28	97853	97776		3.7	10.2

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)
	1.23	1.3	100		0.26	3	7.11	14115

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.23	51.97	97776	9804	99.88	0.174	0.173	0.19	RANDOM	13.796

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]
0.15			-0.37		0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.883
r_dihedral_angle_4_deg	11.585
r_dihedral_angle_3_deg	9.959
r_dihedral_angle_1_deg	5.442
r_scangle_it	2.032
r_sphericity_bonded	1.741
r_sphericity_free	1.582
r_scbond_it	1.291
r_mcangle_it	0.994
r_angle_refined_deg	0.988

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.883
r_dihedral_angle_4_deg	11.585
r_dihedral_angle_3_deg	9.959
r_dihedral_angle_1_deg	5.442
r_scangle_it	2.032
r_sphericity_bonded	1.741
r_sphericity_free	1.582
r_scbond_it	1.291
r_mcangle_it	0.994
r_angle_refined_deg	0.988
r_rigid_bond_restr	0.695
r_mcbond_it	0.545
r_chiral_restr	0.066
r_gen_planes_refined	0.005
r_bond_refined_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2411
Nucleic Acid Atoms
Solvent Atoms	386
Heterogen Atoms	106

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ARP/wARP	model building

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 R01GM133198.