2DUP | pdb_00002dup

Crystal structure of VIP36 exoplasmic/lumenal domain, metal-free form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DUO	PDB ENTRY 2DUO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP, SOAKING	6.5	277	Crystallization: 15% PEG4000, 1.5M NaCl, 0.1M MES (pH6.5), 10mM EDTA, VAPOR DIFFUSION, HANGING DROP, SOAKING, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 171	α = 90
b = 45.2	β = 132.6
c = 117.1	γ = 90

Symmetry
Space Group	C 1 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	95	CCD	ADSC QUANTUM 210		2005-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A

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	2.1	50	93.7	0.083	13.4	3.5	38945	36474			34

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	2.1	2.18	78.9		0.314	3.7	3.4	3041

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2DUO	2.1	20	34622	34622	1828	93.7	0.228	0.228	0.225	0.22	0.278	0.2743	RANDOM	39.27

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]
2.81		3.4	-0.29		2.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.862
r_dihedral_angle_3_deg	15.913
r_dihedral_angle_4_deg	15.569
r_dihedral_angle_1_deg	6.57
r_scangle_it	2.571
r_scbond_it	1.74
r_mcangle_it	1.503
r_angle_refined_deg	1.336
r_mcbond_it	0.912
r_nbtor_refined	0.308
r_symmetry_hbond_refined	0.204
r_symmetry_vdw_refined	0.203
r_nbd_refined	0.193
r_xyhbond_nbd_refined	0.155
r_metal_ion_refined	0.143
r_chiral_restr	0.092
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3913
Nucleic Acid Atoms
Solvent Atoms	194
Heterogen Atoms	23

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing