3H4W | pdb_00003h4w

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. SeMe-derived crystals obtained with initial microseeding with underivatized crystals followed by a series of macroseedings with derivatized enzyme and same conditions., VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.377	α = 90
b = 155.172	β = 90
c = 41.409	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		SAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.9796	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	1.5	77.61	95.15	0.058	8.2689	11.65	52173	52171		3.7	13.6

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)
	1.5	1.58	81.66		0.22	3.19	5.76	6345

Refinement

Statistics
Diffraction ID	Structure Solution Method	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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	1.5	77.59	52168	5234	94.73	0.185	0.184	0.1758	0.2	0.1928	RANDOM	14.295

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]
1.12			-0.61		-0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.275
r_dihedral_angle_4_deg	11.859
r_dihedral_angle_3_deg	10.883
r_dihedral_angle_1_deg	5.111
r_sphericity_free	2.344
r_scangle_it	2.19
r_sphericity_bonded	1.674
r_scbond_it	1.591
r_angle_refined_deg	0.995
r_mcangle_it	0.981

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.275
r_dihedral_angle_4_deg	11.859
r_dihedral_angle_3_deg	10.883
r_dihedral_angle_1_deg	5.111
r_sphericity_free	2.344
r_scangle_it	2.19
r_sphericity_bonded	1.674
r_scbond_it	1.591
r_angle_refined_deg	0.995
r_mcangle_it	0.981
r_rigid_bond_restr	0.877
r_mcbond_it	0.567
r_chiral_restr	0.068
r_bond_refined_d	0.005
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2411
Nucleic Acid Atoms
Solvent Atoms	314
Heterogen Atoms	49

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SHELXD	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.