4IFQ | pdb_00004ifq

Crystal structure of Saccharomyces cerevisiae NUP192, residues 2 to 960 [ScNup192(2-960)]

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		SAD model built using AutoBuild (Phenix) and Buccaneer (CCP4)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	Protein (20 mM Hepes, pH 8.0, 500 mM NaCl, 10% glycerol, 5mM DTT; Reservoir (10% PEG3350, 100mM pottasium iodide); Cryoprotection (30% PEG400 and 25% saturated ammonium sulfate), Vapor Diffusion, Sitting Drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
4.76	74.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.6	α = 90
b = 134.6	β = 90
c = 234.794	γ = 90

Symmetry
Space Group	P 43 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	CCD	ADSC QUANTUM 315	MIRRORS	2012-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9792	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	3.254	50	100	0.136	17.5	8.4	64698	64698			78

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.25	3.29	100		0.969	2.6	8.4	2186

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	SAD	THROUGHOUT	Built using AutoBuild (Phenix) and Buccaneer (CCP4)	3.25	47.76	34573	1930	99.61	0.1905	0.1875	0.1909	0.2431	0.2418	RANDOM	85.2254

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]
2.15			2.15		-4.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.478
r_dihedral_angle_4_deg	18.688
r_dihedral_angle_3_deg	16.906
r_dihedral_angle_1_deg	7.228
r_angle_refined_deg	1.755
r_angle_other_deg	0.885
r_chiral_restr	0.085
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6923
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing