2H57

Crystal structure of human ADP-ribosylation factor-like 6

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZD9	pdb entries 1zd9, 2H16
experimental model	PDB	2H16	pdb entries 1zd9, 2H16

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291	2M ammonium sulfate, 0.2M sodium chloride, 0.1M sodium cacodylate, pH 5.5, vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.058	α = 90
b = 134.885	β = 90
c = 63.884	γ = 90

Symmetry
Space Group	P 21 21 2

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		2006-05-16	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	30	97.9	0.043	17.6	5.3		46561

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		96.2	0.599		5.2

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-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entries 1zd9, 2H16	2	30	46505	1777	97.889	0.207	0.20749	0.2059	0.2453	thin shells	34.198

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]
-1.23			2.829		-1.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.772
r_dihedral_angle_4_deg	21.932
r_dihedral_angle_3_deg	12.527
r_dihedral_angle_1_deg	6.112
r_mcangle_it	3.699
r_scangle_it	3.102
r_mcbond_it	2.54
r_scbond_it	2.274
r_angle_refined_deg	1.393
r_angle_other_deg	1.039
r_mcbond_other	0.59
r_symmetry_vdw_other	0.242
r_symmetry_vdw_refined	0.199
r_nbd_refined	0.196
r_nbd_other	0.191
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.128
r_metal_ion_refined	0.092
r_chiral_restr	0.08
r_nbtor_other	0.079
r_symmetry_hbond_refined	0.067
r_bond_refined_d	0.018
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	3918
Nucleic Acid Atoms
Solvent Atoms	133
Heterogen Atoms	108

Software

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