2B6H | pdb_00002b6h

Structure of human ADP-ribosylation factor 5

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Z6X	PDB entry 1Z6X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	277	25% PEG 4000, 0.2M ammonium sulfate, 0.1M sodium acetate, 3% 6-aminocaproic acid, pH 4.6, vapor diffusion, sitting drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.9	56.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.996	α = 90
b = 81.64	β = 90
c = 84.399	γ = 90

Symmetry
Space Group	C 2 2 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 IV		2005-09-14	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	1.76	50	98.8	0.068		5.9		22373

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	1.76	1.9		95.6	0.306		5.5

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1Z6X	1.764	32.5	22352	1147	99.347	0.202	0.2005	0.21	0.236	0.24	RANDOM	15.61

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]
-0.394			0.6		-0.207

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.78
r_dihedral_angle_4_deg	13.126
r_dihedral_angle_3_deg	11.204
r_dihedral_angle_1_deg	5.87
r_scangle_it	3.527
r_mcangle_it	2.998
r_scbond_it	2.595
r_mcbond_it	2.301
r_mcangle_other	1.799
r_scangle_other	1.765
r_angle_refined_deg	1.4
r_scbond_other	0.894
r_angle_other_deg	0.778
r_mcbond_other	0.723
r_symmetry_vdw_other	0.274
r_symmetry_vdw_refined	0.265
r_nbd_refined	0.213
r_nbd_other	0.191
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.126
r_symmetry_hbond_refined	0.126
r_chiral_restr	0.081
r_nbtor_other	0.08
r_bond_refined_d	0.015
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	1345
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms	40

Software

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