2HUP

Crystal structure of human RAB43 in complex with GDP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2EW1	PDB entry 2EW1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	25% PEG8000, 0.2M NaCl, 0.1M Tris-HCl, pH 8.5, vapor diffusion, sitting drop, temperature 291K, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.8	55.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.447	α = 90
b = 66.447	β = 90
c = 145.116	γ = 120

Symmetry
Space Group	P 32 2 1

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	RIGAKU RAXIS		2006-06-27	M	SINGLE WAVELENGTH
2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE		1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.05	30	99.9	0.116	6.7	9.6		24106

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.05	2.12		100	0.955		8.5

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R	PDB entry 2EW1	2.05	20	23955	2019	99.688	0.237	0.2331	0.2862	thin shells	24.248

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]
0.984	0.492		0.984		-1.477

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.986
r_dihedral_angle_4_deg	16.568
r_dihedral_angle_3_deg	13.451
r_dihedral_angle_1_deg	6.13
r_mcangle_it	3.291
r_scangle_it	3.087
r_mcbond_it	2.402
r_scbond_it	2.377
r_angle_refined_deg	1.41
r_angle_other_deg	0.966
r_mcbond_other	0.715
r_symmetry_vdw_other	0.218
r_nbd_refined	0.209
r_nbd_other	0.199
r_nbtor_refined	0.175
r_symmetry_vdw_refined	0.164
r_symmetry_hbond_refined	0.157
r_xyhbond_nbd_refined	0.131
r_nbtor_other	0.085
r_chiral_restr	0.077
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2455
Nucleic Acid Atoms
Solvent Atoms	76
Heterogen Atoms	61

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction