2H7V | pdb_00002h7v

Co-crystal structure of YpkA-Rac1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2H7O	PDB ID 2H7O, 1MH1
experimental model	PDB	1MH1	PDB ID 2H7O, 1MH1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	100mM HEPES pH 6.5-7.5, 5%-8% PEGMME2000 micro seeding, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.94	68.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.398	α = 92.08
b = 75.519	β = 103.38
c = 99.772	γ = 115.79

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	CCD	ADSC QUANTUM 315	Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror	2005-04-21	M	SINGLE WAVELENGTH
2	1	x-ray		CCD	ADSC QUANTUM 315	Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror	2005-04-21	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.1	NSLS	X29A
2	SYNCHROTRON	NSLS BEAMLINE X29A	1.1	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	2.6	95.78	99.4	0.09	11.8	3.7		51987

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)
1,2	2.6	2.667	99.5		0.418	3

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 (All)	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 ID 2H7O, 1MH1	2.6	95.78	51262	2552	99.39	0.224	0.222	0.222	0.23	0.257	0.26	RANDOM	62.645

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]
7.3	4.77	-3.29	0.97	-0.77	-5.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.492
r_dihedral_angle_3_deg	19.171
r_dihedral_angle_4_deg	17.951
r_dihedral_angle_1_deg	7.039
r_scangle_it	2.504
r_angle_refined_deg	1.666
r_scbond_it	1.579
r_mcangle_it	1.091
r_mcbond_it	0.874
r_angle_other_deg	0.866
r_nbd_refined	0.242
r_symmetry_vdw_other	0.226
r_symmetry_vdw_refined	0.219
r_xyhbond_nbd_refined	0.196
r_nbtor_refined	0.19
r_nbd_other	0.185
r_symmetry_hbond_refined	0.14
r_mcbond_other	0.136
r_nbtor_other	0.093
r_chiral_restr	0.084
r_xyhbond_nbd_other	0.059
r_metal_ion_refined	0.034
r_bond_refined_d	0.017
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7058
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	58

Software

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