3BRW

Structure of the Rap-RapGAP complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SRQ	PDB ENTRY 1SRQ for Rap1GAP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	285	8-11% PEG 2000 MME, 100mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

Crystal Properties
Matthews coefficient	Solvent content
5.061804	75.700363

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 209.723	α = 90
b = 209.723	β = 90
c = 108.217	γ = 120

Symmetry
Space Group	P 31 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	100	CCD	MARMOSAIC 225 mm CCD		2006-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.97916	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	3.4	182.57	99.2	0.087	0.087	15.48	6.5	37639	37639	3	-3

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)
	3.4	3.5	98.4		0.335	3.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1SRQ for Rap1GAP	3.4	48.08	37637	35759	1878	99.16	0.23624	0.23389	0.28043	RANDOM	97.485

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]
4.21	2.1		4.21		-6.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.009
r_dihedral_angle_3_deg	19.627
r_dihedral_angle_4_deg	16.589
r_dihedral_angle_1_deg	6.007
r_angle_refined_deg	1.128
r_scangle_it	0.84
r_mcangle_it	0.798
r_scbond_it	0.485
r_mcbond_it	0.439
r_nbtor_refined	0.305
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.181
r_xyhbond_nbd_refined	0.15
r_symmetry_hbond_refined	0.083
r_chiral_restr	0.077
r_metal_ion_refined	0.043
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9422
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms	33

Software

Software
Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection