1U29 | pdb_00001u29

Triglycine variant of the ARNO Pleckstrin Homology Domain in complex with Ins(1,4,5)P3

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	PEG 4000, Hepes, 10% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.998	α = 90
b = 56.378	β = 90
c = 57.091	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MARRESEARCH		2001-03-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE		1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	20	99.6			13456	13437		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.85	99.4

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 (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	MOLECULAR REPLACEMENT	THROUGHOUT	1FGY	1.8	20	12727	12727	660	99.83	0.2304	0.23038	0.22877	0.24	0.26225	0.27	RANDOM	25.493

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]
0.93			-1.68		0.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.02
r_scangle_it	2.919
r_scbond_it	1.902
r_mcangle_it	1.4
r_angle_refined_deg	1.203
r_angle_other_deg	0.748
r_mcbond_it	0.747
r_symmetry_vdw_other	0.305
r_nbd_other	0.241
r_nbd_refined	0.177
r_symmetry_hbond_refined	0.137
r_xyhbond_nbd_refined	0.134
r_symmetry_vdw_refined	0.103
r_nbtor_other	0.08
r_chiral_restr	0.072
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	977
Nucleic Acid Atoms
Solvent Atoms	89
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing