2G6B | pdb_00002g6b

Crystal structure of human RAB26 in complex with a GTP analogue

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1G16	pdb entry 1G16_A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	25% PEG3350, 0.1M NH4SO4, 0.1M HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.4	49.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.368	α = 90
b = 55.614	β = 90
c = 92.3	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	IMAGE PLATE	RIGAKU RAXIS		2006-02-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	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	30	99.5	0.173	4.4	7.6		12581

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	2.07		95.7	0.841		6.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	pdb entry 1G16_A	2	30	12491	609	99.673	0.213	0.2096	0.22	0.2769	0.29	19.721

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]
0.059			0.615		-0.674

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.279
r_dihedral_angle_4_deg	17.854
r_dihedral_angle_3_deg	13.782
r_dihedral_angle_1_deg	5.4
r_scangle_it	3.249
r_mcangle_it	3.22
r_mcbond_it	2.367
r_scbond_it	2.342
r_angle_refined_deg	1.461
r_angle_other_deg	1.018
r_mcbond_other	0.558
r_symmetry_hbond_refined	0.311
r_symmetry_vdw_other	0.31
r_nbd_other	0.209
r_symmetry_vdw_refined	0.202
r_nbd_refined	0.2
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.167
r_nbtor_other	0.087
r_chiral_restr	0.08
r_metal_ion_refined	0.027
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1272
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms	37

Software

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