7L92 | pdb_00007l92

C1B domain of Protein kinase C in complex with diacylglycerol and dodecyl 2-(trimethylammonio)ethyl phosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PTQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277.15	Screen condition: 0.2 M Ammonium acetate 0.1 M Sodium phosphate 15% Isopropanol pH 6.8 Drop conditions: For seed crystals Protein: 2 mM in MES pH 6.5, 150 mM KCl Dodecylphosphocholine: 20 mM 1,2-dioctanoyl-sn-glycerol: 2.5 mM Final drop Protein: 2 mM in MES pH 6.5, 150 mM KCl Dodecylphosphocholine: 10 mM 1,2-dioctanoyl-sn-glycerol: 2.5 mM

Crystal Properties
Matthews coefficient	Solvent content
3.42	64.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.068	α = 90
b = 89.068	β = 90
c = 218.679	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	PIXEL	DECTRIS PILATUS 6M		2020-11-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.03322	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	44.6	99.1	0.07	0.991	6.8	2.8		64618

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.78			0.613	0.528

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1ptq	1.75	28.96	1.96	64599	3397	99.07	0.216	0.2142	0.22	0.246	0.25	40.2307

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3319
Nucleic Acid Atoms
Solvent Atoms	231
Heterogen Atoms	447

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOLREP	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.