3HZJ | pdb_00003hzj

Crystal structure of the RabGAP domain of the RABGAP1L protein

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6	291	16% PEG3350, 0.2M potassium chloride, 1:100 (w/w) Dispase., pH 6.0, vapor diffusion, hanging drop, temperature 291K
2		5.8	291	15% PEG3350, 0.2M potassium chloride, 1:100 (w/w) Dispase., pH 5.8, vapor diffusion, hanging drop, temperature 291K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.086	α = 90
b = 64.571	β = 90
c = 290.255	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARCCD 300		2009-05-18	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARCCD 300	2009-05-17	2009-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.92015	CLSI	08ID-1
2	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97959	CLSI	08ID-1

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
1,2	2.3	30	88.4	0.053	31.893	3.5		38070

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)
	2.3	2.38	49.8		0.233		2

Refinement

Statistics
Diffraction ID	Structure Solution Method	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	SAD	2.3	20	38070	1191	92.3	0.245	0.244	0.2399	0.274	0.2704	THIN SHELLS (SFTOOLS)	43.62

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]
0.337			1.886		-2.224

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.129
r_dihedral_angle_4_deg	16.103
r_dihedral_angle_3_deg	14.336
r_dihedral_angle_1_deg	4.937
r_scangle_it	2.255
r_scbond_it	1.754
r_angle_refined_deg	1.117
r_angle_other_deg	0.875
r_mcangle_it	0.706
r_mcbond_it	0.361
r_mcbond_other	0.101
r_chiral_restr	0.062
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
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	6428
Nucleic Acid Atoms
Solvent Atoms	13
Heterogen Atoms	32

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling