3C72 | pdb_00003c72

Engineered RabGGTase in complex with a peptidomimetic inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LTX	PDB ENTRY 1LTX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	284	14% (w/v) PEG 3350, 0.2 M Ca-Acetate, 0.1 M HEPES, cocrystallization with 5 mM inhibitor, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.192	α = 90
b = 91.671	β = 90
c = 115.439	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	Si(111) monochromator	2006-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9797	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	2.3	20	99.7	5.2	20	5.7		31830		4.7	50

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	2.3	2.4	100		40.7	4.7	5.8	3742

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 1LTX	2.3	19.88	30241	1587	99.95	0.19242	0.18908	0.19	0.25617	0.26	RANDOM	31.217

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	37.575
r_dihedral_angle_4_deg	19.655
r_dihedral_angle_3_deg	18.289
r_dihedral_angle_1_deg	6.726
r_scangle_it	2.958
r_scbond_it	2.1
r_angle_refined_deg	1.622
r_mcangle_it	1.451
r_angle_other_deg	1.061
r_mcbond_it	0.878
r_symmetry_vdw_other	0.224
r_nbd_refined	0.217
r_nbd_other	0.195
r_mcbond_other	0.195
r_xyhbond_nbd_refined	0.194
r_nbtor_refined	0.185
r_metal_ion_refined	0.158
r_symmetry_hbond_refined	0.103
r_nbtor_other	0.095
r_chiral_restr	0.093
r_symmetry_vdw_refined	0.084
r_bond_refined_d	0.019
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4988
Nucleic Acid Atoms
Solvent Atoms	191
Heterogen Atoms	47

Software

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