4GTV

Engineered RabGGTase in complex with BMS analogue 13

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	285	RabGGTase in 20mM Hepes pH7.2, 100mM NaCl and 2mM DTT was mixed with 15% PEG3350, 0.2M Ca Acetate, 0.1M Hepes pH7.2. The obtained crystals was soaked with 20% PEG3350, 0.2M Ca Acetate, 5% Glycerol in the presence of 1mM inhibitor for 12 hour, VAPOR DIFFUSION, HANGING DROP, temperature 285K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.625	α = 90
b = 90.741	β = 90
c = 115.539	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		2009-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9879	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	1.95	19.99	98.7	0.062	16.9	4.9	51813	51134			32.1

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)
1	1.95	2	98.4		0.361	5.2	4.9

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	3DSS	1.95	19.99	51813	48526	2565	98.73	0.17045	0.16835	0.21143	RANDOM	27.672

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]
0.92			-0.64		-0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.14
r_dihedral_angle_4_deg	19.991
r_dihedral_angle_3_deg	14.879
r_dihedral_angle_1_deg	5.341
r_angle_other_deg	4.188
r_scangle_it	3.581
r_scbond_it	2.291
r_mcbond_other	2.193
r_mcangle_it	1.791
r_angle_refined_deg	1.121
r_mcbond_it	1.024
r_symmetry_vdw_other	0.27
r_nbd_other	0.233
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.212
r_xyhbond_nbd_other	0.202
r_symmetry_vdw_refined	0.2
r_symmetry_hbond_refined	0.186
r_nbtor_refined	0.177
r_nbtor_other	0.106
r_chiral_restr	0.072
r_metal_ion_refined	0.071
r_symmetry_metal_ion_refined	0.059
r_bond_refined_d	0.009
r_gen_planes_other	0.005
r_gen_planes_refined	0.004
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	4986
Nucleic Acid Atoms
Solvent Atoms	379
Heterogen Atoms	48

Software

Software
Software Name	Purpose
MOSFLM	data reduction
PHASES	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling