2F7S | pdb_00002f7s

The crystal structure of human Rab27b bound to GDP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OIV	PDB entry 1OIV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	20%(v/v) isopropanol, 25%(v/v)PEG 4K, 0.1M sodium citrate, 0.1 M bistris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.469	α = 90
b = 64.023	β = 90
c = 153.32	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	ADSC QUANTUM 210		2005-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	0.978	APS	17-ID

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	2.69	50	99.3	0.05	37.6	6.6	15658	15658	1	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)
	2.69	2.82	96.1		0.21	5.69	5.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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 1OIV	2.7	50	1	14687	803	99.04	0.24765	0.24529	0.2425	0.29248	0.2939	RANDOM	57.722

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]
-0.72			6.17		-5.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.488
r_dihedral_angle_3_deg	20.28
r_dihedral_angle_4_deg	19.123
r_dihedral_angle_1_deg	6.359
r_angle_refined_deg	1.486
r_nbtor_refined	0.315
r_nbd_refined	0.23
r_xyhbond_nbd_refined	0.181
r_symmetry_vdw_refined	0.174
r_metal_ion_refined	0.095
r_chiral_restr	0.091
r_symmetry_hbond_refined	0.043
r_bond_refined_d	0.013
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2887
Nucleic Acid Atoms
Solvent Atoms	13
Heterogen Atoms	58

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing