2HEI

Crystal structure of human RAB5B in complex with GDP

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1N6I	PDB ENTRY 1N6I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	291	25% P3350, 0.1M NaOAc, pH 4.5, vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.1	37.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.302	α = 90
b = 78.37	β = 90
c = 95.501	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 4		2006-05-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1		CHESS	F1

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	1.5	50	100	0.058	9.2	7		50161

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)
	1.5	1.55		100	0.679		6.7

Refinement

Statistics
Diffraction ID	Structure Solution 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	PDB ENTRY 1N6I	1.55	30	45443	2875	99.184	0.264	0.2622	0.2936	thin shells	15.121

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]
-0.375			0.517		-0.143

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.633
r_dihedral_angle_4_deg	14.429
r_dihedral_angle_3_deg	12.151
r_dihedral_angle_1_deg	6.085
r_scangle_it	3.232
r_mcangle_it	2.907
r_scbond_it	2.466
r_mcbond_it	2.432
r_angle_refined_deg	1.488
r_angle_other_deg	1.139
r_mcbond_other	0.687
r_symmetry_vdw_other	0.269
r_symmetry_vdw_refined	0.229
r_nbd_refined	0.21
r_nbd_other	0.194
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.131
r_chiral_restr	0.108
r_symmetry_hbond_refined	0.106
r_nbtor_other	0.086
r_bond_refined_d	0.018
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2568
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	72

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ARP/wARP	model building
MolProbity	model building