2H7O

Crystal structure of the Rho-GTPase binding domain of YpkA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	10.5	276	100mM CAPs pH 10.5, 140mM-180mM NaCl, 16%-18% PEG1500 Micro Seeding, VAPOR DIFFUSION, HANGING DROP, temperature 276K

Crystal Properties
Matthews coefficient	Solvent content
3.13	60.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.009	α = 90
b = 60.009	β = 90
c = 402.022	γ = 120

Symmetry
Space Group	P 65 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	CCD	ADSC QUANTUM 315	Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror	2004-11-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.979	NSLS	X29A

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	99	98.5	0.045	33.1	9		30187

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	2.054	90.29		0.361	3.2

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-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2	33.88	28539	1485	98.5	0.209	0.209	0.208	0.237	RANDOM	40.659

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]
0.07	0.03		0.07		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.356
r_dihedral_angle_4_deg	17.347
r_dihedral_angle_3_deg	16.453
r_dihedral_angle_1_deg	6.803
r_scangle_it	4.494
r_scbond_it	3.283
r_mcangle_it	1.921
r_angle_refined_deg	1.739
r_mcbond_it	1.664
r_angle_other_deg	0.978
r_symmetry_vdw_refined	0.365
r_mcbond_other	0.336
r_symmetry_vdw_other	0.308
r_xyhbond_nbd_other	0.24
r_symmetry_hbond_refined	0.234
r_nbd_refined	0.232
r_xyhbond_nbd_refined	0.231
r_nbd_other	0.189
r_nbtor_refined	0.176
r_chiral_restr	0.121
r_nbtor_other	0.089
r_bond_refined_d	0.022
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2169
Nucleic Acid Atoms
Solvent Atoms	276
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing
RESOLVE	phasing