2NZ8 | pdb_00002nz8

N-terminal DHPH cassette of Trio in complex with nucleotide-free Rac1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NTY	residues 1231-1390 of PDB entry 1NTY and residues 1-177 of PDB entry 1FOE
experimental model	PDB	1FOE	residues 1231-1390 of PDB entry 1NTY and residues 1-177 of PDB entry 1FOE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	291	100 mM sodium cacodylate pH 5.5 to 6.5, 14 to 18% (w/v) PEG 8000, and 300-500 mM calcium acetate, pH 6.0, VAPOR DIFFUSION, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.492	α = 90
b = 108.558	β = 90
c = 53.416	γ = 90

Symmetry
Space Group	P 21 21 2

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		2004-10-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0712	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	20	99.6	0.069	15.6	5.4	39574	39416		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.07	99.8		0.524	3.53	4.2	3903

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	residues 1231-1390 of PDB entry 1NTY and residues 1-177 of PDB entry 1FOE	2	19.41	39416	38900	1968	99.61	0.225	0.223	0.2228	0.249	0.2456	RANDOM	41.241

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]
0.01			0.2		-0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.698
r_dihedral_angle_4_deg	16.585
r_dihedral_angle_3_deg	15.149
r_dihedral_angle_1_deg	5.078
r_scangle_it	1.913
r_scbond_it	1.26
r_angle_refined_deg	1.138
r_mcangle_it	0.848
r_mcbond_it	0.52
r_nbtor_refined	0.3
r_symmetry_vdw_refined	0.2
r_nbd_refined	0.19
r_xyhbond_nbd_refined	0.148
r_symmetry_hbond_refined	0.094
r_chiral_restr	0.083
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3663
Nucleic Acid Atoms
Solvent Atoms	242
Heterogen Atoms

Software

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