2ZII | pdb_00002zii

Crystal Structure of Yeast Vps74-N-term Truncation Variant

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	15% PEG 3350, 5% glycerol, 10mM citrate, 0.75mM KCl, 50mM EGTA, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.46	64.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.081	α = 90
b = 104.081	β = 90
c = 292.759	γ = 120

Symmetry
Space Group	P 31 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	100	CCD	ADSC QUANTUM 270		2007-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1	0.91790	CHESS	F1

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	3.05	50	99.8	0.142	5.6	6.1		35872			49.3

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)
	3.05	3.16	100		0.529		6.2	3524

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 (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 2ZIH	3.05	49.1	35793	1790	99.73	0.223	0.22	0.2186	0.281	0.2778	RANDOM	42.122

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]
0.87	0.43		0.87		-1.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.412
r_dihedral_angle_4_deg	22.473
r_dihedral_angle_3_deg	21.659
r_dihedral_angle_1_deg	6.888
r_scangle_it	2.395
r_angle_refined_deg	1.663
r_scbond_it	1.426
r_mcangle_it	1.134
r_mcbond_it	0.62
r_nbtor_refined	0.32
r_nbd_refined	0.244
r_symmetry_vdw_refined	0.193
r_xyhbond_nbd_refined	0.18
r_symmetry_hbond_refined	0.153
r_chiral_restr	0.112
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8588
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling