9GH3 | pdb_00009gh3

pleckstrin homology domain interacting protein with crystallization epitope mutations L1408N:R1409E

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MB3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20% PEG3000 0.1M citrate pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.77	α = 90
b = 26.98	β = 100.56
c = 55.83	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	100	PIXEL	DECTRIS PILATUS 6M		2016-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9282	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.16	41.21	94.7	0.999	10.5	2.7		40440

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.16	1.19			0.876

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.19	41.21	37594	1868	94.424	0.18	0.1791	0.18	0.2022	0.2	18.842

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]
0.151		0.738	0.197		-0.582

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.204
r_dihedral_angle_2_deg	11.902
r_dihedral_angle_3_deg	11.332
r_lrange_it	5.52
r_dihedral_angle_1_deg	4.726
r_scangle_it	4.04
r_scbond_it	2.781
r_angle_refined_deg	2.041
r_mcangle_it	1.598
r_mcbond_it	1.178

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.204
r_dihedral_angle_2_deg	11.902
r_dihedral_angle_3_deg	11.332
r_lrange_it	5.52
r_dihedral_angle_1_deg	4.726
r_scangle_it	4.04
r_scbond_it	2.781
r_angle_refined_deg	2.041
r_mcangle_it	1.598
r_mcbond_it	1.178
r_nbtor_refined	0.297
r_xyhbond_nbd_refined	0.203
r_nbd_refined	0.2
r_symmetry_xyhbond_nbd_refined	0.199
r_symmetry_nbd_refined	0.169
r_chiral_restr	0.11
r_bond_refined_d	0.015
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1053
Nucleic Acid Atoms
Solvent Atoms	220
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	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.