1YZG | pdb_00001yzg

Structure of Human ADP-ribosylation factor-like 8

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	PEG 3350, Sodium dihydrogen phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.2	43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.725	α = 90
b = 48.137	β = 103.45
c = 51.371	γ = 90

Symmetry
Space Group	P 1 21 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 IV		2005-02-15	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	99.9	0.077		3.4	12238	12238			21.4

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	100		0.211	3.5	2.16	1220

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1RRF	2	30	12228	11611	617	99.9	0.2261	0.2261	0.226	0.23	0.27	RANDOM	21.581

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]
-0.57		0.55	-0.16		0.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.481
r_dihedral_angle_4_deg	23.474
r_dihedral_angle_3_deg	15.445
r_dihedral_angle_1_deg	6.096
r_scangle_it	2.79
r_scbond_it	1.973
r_angle_refined_deg	1.509
r_mcangle_it	1.405
r_mcbond_it	0.909
r_nbtor_refined	0.304
r_nbd_refined	0.223
r_symmetry_hbond_refined	0.215
r_symmetry_vdw_refined	0.203
r_xyhbond_nbd_refined	0.176
r_chiral_restr	0.109
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1341
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms	28

Software

Software
Software Name	Purpose
CrystalClear	data collection
CrystalClear	data reduction
AMoRE	phasing
REFMAC	refinement
CrystalClear	data scaling