3DSV | pdb_00003dsv

Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with mono-prenylated peptide Ser-Cys-Ser-Cys(GG) derivated from Rab7

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DSS	PDB ENTRY 3DSS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	284	14% (w/v) PEG 3350, 0.2M Ca(OAc)2, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.035	α = 90
b = 90.613	β = 90
c = 114.376	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	MARMOSAIC 225 mm CCD		2007-09-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9999	SLS	X10SA

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	2.1	30	99.9	0.085	31	18.5	41395	41339		5	30

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)
	2.1	2.2	99.7		0.379	11.1	16.5	5293

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3DSS	2.1	29.2	39268	2071	99.92	0.15231	0.14927	0.16	0.21114	0.22	RANDOM	25.886

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]
1.73			-0.44		-1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.766
r_dihedral_angle_4_deg	19.937
r_dihedral_angle_3_deg	16.373
r_dihedral_angle_1_deg	12.981
r_angle_other_deg	3.745
r_scangle_it	3.701
r_scbond_it	2.394
r_mcangle_it	1.968
r_angle_refined_deg	1.456
r_mcbond_it	1.1
r_mcbond_other	1.034
r_symmetry_hbond_refined	0.443
r_nbd_other	0.234
r_symmetry_vdw_other	0.228
r_nbd_refined	0.22
r_symmetry_vdw_refined	0.208
r_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.182
r_nbtor_other	0.107
r_chiral_restr	0.104
r_xyhbond_nbd_other	0.074
r_metal_ion_refined	0.059
r_symmetry_metal_ion_refined	0.017
r_bond_refined_d	0.011
r_gen_planes_other	0.006
r_gen_planes_refined	0.005
r_bond_other_d
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	5093
Nucleic Acid Atoms
Solvent Atoms	495
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing