3BYI

Crystal structure of human Rho GTPase activating protein 15 (ARHGAP15)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TX4	assembly of PDB entries 1TX4, 1OW3, 1RGP, 2NGR, 1GRN, 1F7C, 1AM4
experimental model	PDB	1OW3	assembly of PDB entries 1TX4, 1OW3, 1RGP, 2NGR, 1GRN, 1F7C, 1AM4
experimental model	PDB	1RGP	assembly of PDB entries 1TX4, 1OW3, 1RGP, 2NGR, 1GRN, 1F7C, 1AM4
experimental model	PDB	2NGR	assembly of PDB entries 1TX4, 1OW3, 1RGP, 2NGR, 1GRN, 1F7C, 1AM4
experimental model	PDB	1GRN	assembly of PDB entries 1TX4, 1OW3, 1RGP, 2NGR, 1GRN, 1F7C, 1AM4
experimental model	PDB	1F7C	assembly of PDB entries 1TX4, 1OW3, 1RGP, 2NGR, 1GRN, 1F7C, 1AM4
experimental model	PDB	1AM4	assembly of PDB entries 1TX4, 1OW3, 1RGP, 2NGR, 1GRN, 1F7C, 1AM4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	293	2.4M Na malate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.618	α = 90
b = 130.142	β = 90
c = 62.477	γ = 90

Symmetry
Space Group	P 21 21 2

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		2007-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.95362	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	2.25	50	100	0.086	0.086	15.4	7.1	47518	47518

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.37	99.9		0.823	0.823	0.9	6.9	6829

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 (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	assembly of PDB entries 1TX4, 1OW3, 1RGP, 2NGR, 1GRN, 1F7C, 1AM4	2.25	50	47463	47463	2418	99.95	0.191	0.191	0.188	0.19	0.244	0.25	RANDOM	40.047

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]
-1.04			3.01		-1.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.647
r_dihedral_angle_4_deg	20.527
r_dihedral_angle_3_deg	14.796
r_scangle_it	6.794
r_dihedral_angle_1_deg	5.688
r_scbond_it	5.269
r_mcangle_it	2.915
r_mcbond_it	2.023
r_angle_refined_deg	1.379
r_angle_other_deg	1.006
r_mcbond_other	0.528
r_symmetry_vdw_refined	0.279
r_symmetry_vdw_other	0.236
r_nbd_refined	0.218
r_symmetry_hbond_refined	0.18
r_nbtor_refined	0.178
r_nbd_other	0.177
r_xyhbond_nbd_refined	0.164
r_nbtor_other	0.086
r_chiral_restr	0.082
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6602
Nucleic Acid Atoms
Solvent Atoms	197
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOSFLM	data reduction