4QJ4 | pdb_00004qj4

Structure of a fragment of human phospholipase C-beta3 delta472-569, bound to IP3 and in complex with Galphaq

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OHM	PDB ENTRY 3OHM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277.15	100 mM BisTris, 200 mM NaCl, 8% (v/v) PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 201.923	α = 90
b = 89.191	β = 101.7
c = 92.639	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	MARMOSAIC 300 mm CCD		2014-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.979	APS	21-ID-D

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	3.3	30	85.6	0.221	8.71	3.7	21343	21289	-2000	-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	3.3	3.36	64.6		0.48	3.27	2.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB ENTRY 3OHM	3.3	29.4	20279	20279	1010	85.14	0.21063	0.2078	0.21	0.26665	0.26	RANDOM	72.003

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		-0.06	0.41		-0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.121
r_dihedral_angle_3_deg	14.406
r_dihedral_angle_4_deg	13.497
r_dihedral_angle_1_deg	5.054
r_long_range_B_refined	3.036
r_long_range_B_other	3.036
r_mcangle_it	1.686
r_mcangle_other	1.686
r_scangle_other	1.266
r_angle_refined_deg	0.929
r_mcbond_it	0.926
r_mcbond_other	0.926
r_angle_other_deg	0.676
r_scbond_it	0.676
r_scbond_other	0.676
r_chiral_restr	0.05
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8646
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	59

Software

Software
Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	phasing