3MSX | pdb_00003msx

Crystal structure of RhoA.GDP.MgF3 in complex with GAP domain of ArhGAP20

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Crystallization drop was 1:1 mixture of protein dissolved in 20 mM Tris, pH 8.5, 100 mM NaCl, 5 mM NaF, 5 mM MgCl2, 5mM 2-mercaptoethanol and 20 w/v% PEG 8000, 0.2 M NaCl, 0.17 M NH4Cl, 0.1 M phosphate citrate buffer. The crystallization reservoir was 20 w/v% PEG 8000, 0.2 M NaCl, 0.17 M NH4Cl, 0.1 M phosphate citrate buffer, vapor diffusion, sitting drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.057	α = 90
b = 88.977	β = 90
c = 137.725	γ = 90

Symmetry
Space Group	C 2 2 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	CCD	MARMOSAIC 225 mm CCD		2008-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	0.97166	APS	22-BM

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	1.65	40	99.9	0.061	12.3	7.2		41890

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)
	1.65	1.689	100		0.12		7.3	858

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 (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	1.65	27.23	41890	2229	85.44	0.196	0.195	0.1955	0.219	0.2194	RANDOM	37.867

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]
-0.55			-0.57		1.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.383
r_dihedral_angle_4_deg	18.232
r_dihedral_angle_3_deg	14.694
r_scangle_it	5.797
r_dihedral_angle_1_deg	5.116
r_scbond_it	4.872
r_mcangle_it	2.895
r_mcbond_it	2.344
r_angle_refined_deg	1.503
r_nbtor_refined	0.31
r_nbd_refined	0.218
r_symmetry_vdw_refined	0.199
r_symmetry_hbond_refined	0.188
r_xyhbond_nbd_refined	0.156
r_chiral_restr	0.094
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2929
Nucleic Acid Atoms
Solvent Atoms	222
Heterogen Atoms	33

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection