3DSX | pdb_00003dsx

Crystal structure of RabGGTase(DELTA LRR; DELTA IG)in complex with di-prenylated peptide Ser-Cys(GG)-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	DB 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, 2.5% (v/v)DMSO, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.354	α = 90
b = 91.153	β = 90
c = 114.591	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		2007-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9841	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	99.8	0.057	23.4	7.2	41909	41826		5	39

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	100		0.391	6.9	7.4	5348

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	DB ENTRY 3DSS	2.1	29.37	39725	2101	99.85	0.17056	0.16753	0.18	0.22942	0.24	RANDOM	30.065

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.612
r_dihedral_angle_4_deg	18.592
r_dihedral_angle_3_deg	16.294
r_dihedral_angle_1_deg	5.676
r_scangle_it	3.576
r_scbond_it	2.397
r_mcangle_it	1.867
r_angle_refined_deg	1.285
r_mcbond_it	1.166
r_angle_other_deg	0.846
r_mcbond_other	0.699
r_symmetry_hbond_refined	0.263
r_symmetry_vdw_other	0.262
r_nbd_refined	0.215
r_nbtor_refined	0.182
r_nbd_other	0.18
r_xyhbond_nbd_refined	0.175
r_symmetry_vdw_refined	0.156
r_metal_ion_refined	0.099
r_nbtor_other	0.087
r_chiral_restr	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
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	5089
Nucleic Acid Atoms
Solvent Atoms	297
Heterogen Atoms	22

Software

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