2P2L | pdb_00002p2l

Rac1-GDP-Zinc Complex

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	100mM MES pH6.0, 15mM ZnSO4, 10% PEGMME 550., VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.55	65.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.727	α = 90
b = 89.727	β = 90
c = 190.618	γ = 120

Symmetry
Space Group	P 32 2 1

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	MAR CCD 165 mm	Double crystal monochromator. Si(111) or Si(220) options. Sagitall focusing. Cylindrically bent ULE mirror with Pt and Rh coating.	2007-01-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X3A	1.284	NSLS	X3A

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	1.9	77.62	99.9	0.1	10	7.7		70803

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	1.9	1.97	100		0.512	3.7	7.8

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	and molecular replacement	THROUGHOUT	1MH1	1.9	77.62	67009	3560	99.61	0.17733	0.17568	0.19	0.20808	0.21	RANDOM	27.003

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]
0.63	0.31		0.63		-0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.036
r_dihedral_angle_4_deg	21.019
r_dihedral_angle_3_deg	15.685
r_dihedral_angle_1_deg	6.697
r_scangle_it	3.447
r_scbond_it	2.412
r_angle_refined_deg	1.627
r_mcangle_it	1.474
r_mcbond_it	1.278
r_angle_other_deg	0.911
r_symmetry_vdw_other	0.311
r_symmetry_hbond_refined	0.264
r_nbd_refined	0.225
r_mcbond_other	0.223
r_xyhbond_nbd_refined	0.193
r_nbd_other	0.192
r_nbtor_refined	0.178
r_symmetry_vdw_refined	0.147
r_xyhbond_nbd_other	0.115
r_chiral_restr	0.105
r_nbtor_other	0.089
r_symmetry_metal_ion_refined	0.089
r_metal_ion_refined	0.052
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4141
Nucleic Acid Atoms
Solvent Atoms	804
Heterogen Atoms	92

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction