1Z06 | pdb_00001z06

GppNHp-Bound Rab33 GTPase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Polyalanine Rab5c GTPase

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	20% PEG 6000, 10% Glycerol, 1M Lithium Chlroride, 50mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.75	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.194	α = 90
b = 56.194	β = 90
c = 55.039	γ = 120

Symmetry
Space Group	P 32

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 300 mm plate	osmic mirror	2003-02-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R

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	1.8	50	96.7	0.057	29	5		17431			31.5

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)
	1.8	1.85	84.2		0.249	7.7	5	1240

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 (All)	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	Polyalanine Rab5c GTPase	1.81	8	17435	16353	879	97.52	0.207	0.19082	0.18946	0.2	0.21794	0.23	RANDOM	22.211

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]
-0.43	-0.21		-0.43		0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.74
r_dihedral_angle_4_deg	15.906
r_dihedral_angle_3_deg	12.23
r_dihedral_angle_1_deg	5.458
r_scangle_it	1.915
r_scbond_it	1.349
r_angle_refined_deg	1.275
r_mcangle_it	1.059
r_mcbond_it	0.965
r_angle_other_deg	0.826
r_symmetry_vdw_other	0.261
r_nbd_refined	0.205
r_nbd_other	0.182
r_nbtor_refined	0.175
r_symmetry_hbond_refined	0.131
r_xyhbond_nbd_refined	0.129
r_mcbond_other	0.123
r_xyhbond_nbd_other	0.096
r_symmetry_vdw_refined	0.096
r_nbtor_other	0.082
r_chiral_restr	0.078
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_refined
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	1269
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing