3PZ3 | pdb_00003pz3

Crystal structure of RabGGTase(DELTA LRR; DELTA IG) in Complex with BMS-analogue 14

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	284	14% (w/v) PEG3350, 0.2 M Ca(OAc)2, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 284K

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.732	α = 90
b = 91.332	β = 90
c = 114.652	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		2009-05-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9770	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	20	99	0.041	20.5	3.7	48077	47598		5	37.3

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	2.1	99.6		0.354	4.8	3.7	6416

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	3DSS	2	20	45177	2389	99.07	0.18072	0.17849	0.19	0.22368	0.23	RANDOM	36.218

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]
1.15			-0.28		-0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.915
r_dihedral_angle_4_deg	18.751
r_dihedral_angle_3_deg	15.386
r_dihedral_angle_1_deg	5.075
r_scangle_it	4.278
r_angle_other_deg	4.179
r_mcbond_other	3.066
r_scbond_it	2.697
r_mcangle_it	2.078
r_mcbond_it	1.207
r_angle_refined_deg	1.194
r_xyhbond_nbd_other	0.364
r_symmetry_vdw_other	0.306
r_nbd_other	0.231
r_nbd_refined	0.214
r_symmetry_vdw_refined	0.205
r_xyhbond_nbd_refined	0.191
r_nbtor_refined	0.182
r_metal_ion_refined	0.165
r_symmetry_hbond_refined	0.151
r_nbtor_other	0.109
r_chiral_restr	0.074
r_bond_refined_d	0.01
r_gen_planes_other	0.006
r_gen_planes_refined	0.004
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5006
Nucleic Acid Atoms
Solvent Atoms	333
Heterogen Atoms	56

Software

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