2OCB

Crystal structure of human RAB9B in complex with a GTP analogue

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	2M ammonium sulfate, 0.2M sodium chloride, 0.1M HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.5	65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.43	α = 90
b = 70.43	β = 90
c = 97.715	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		2006-08-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E	1.5418

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	2.2	30	99.9	0.107	10.2	6.1		14718

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)
	2.2	2.28		100	0.725		5.8

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 1wms	2.2	23.051	14665	738	99.83	0.215	0.2135	0.2531	random	31.515

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]
2.436	1.218		2.436		-3.654

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.515
r_dihedral_angle_3_deg	13.579
r_dihedral_angle_4_deg	11.395
r_dihedral_angle_1_deg	6.076
r_mcangle_it	3.792
r_scangle_it	3.185
r_mcbond_it	2.729
r_scbond_it	2.399
r_angle_refined_deg	1.416
r_angle_other_deg	0.95
r_mcbond_other	0.701
r_symmetry_vdw_other	0.213
r_nbd_other	0.196
r_nbd_refined	0.182
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.167
r_symmetry_hbond_refined	0.166
r_symmetry_vdw_refined	0.12
r_nbtor_other	0.084
r_chiral_restr	0.076
r_bond_refined_d	0.017
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	1368
Nucleic Acid Atoms
Solvent Atoms	37
Heterogen Atoms	40

Software

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