3EO2 | pdb_00003eo2

Crystal structure of the RhoGEF domain of human neuroepithelial cell-transforming gene 1 protein

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z0Q	pdb entry 2Z0Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8		1.0M sodium citrate, 0.1M sodium cacodylate, 5% ethylene glycol, crystallized in the presence of 1:100 (w/w) subtilisin, pH 4.8, vapor diffusion, hanging drop

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.629	α = 90
b = 95.629	β = 90
c = 62.887	γ = 120

Symmetry
Space Group	P 64

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 300 mm CCD		2008-08-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97945	APS	23-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	2.6	50	95.1	0.095	12.9	8.8		9673

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	2.6	2.69	65.3		0.526		2.3	645

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 2Z0Q	2.6	30	9653	465	94.898	0.215	0.213	0.24	0.25	0.27	RANDOM	33.152

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]
-1.752	-0.876		-1.752		2.628

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.023
r_dihedral_angle_4_deg	23.591
r_dihedral_angle_3_deg	15.378
r_dihedral_angle_1_deg	4.982
r_scangle_it	1.845
r_mcangle_it	1.578
r_angle_refined_deg	1.123
r_scbond_it	1.063
r_mcbond_it	0.885
r_angle_other_deg	0.863

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.023
r_dihedral_angle_4_deg	23.591
r_dihedral_angle_3_deg	15.378
r_dihedral_angle_1_deg	4.982
r_scangle_it	1.845
r_mcangle_it	1.578
r_angle_refined_deg	1.123
r_scbond_it	1.063
r_mcbond_it	0.885
r_angle_other_deg	0.863
r_mcbond_other	0.129
r_chiral_restr	0.059
r_bond_refined_d	0.014
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1468
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	1

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling

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.