4Q9T | pdb_00004q9t

Crystal structure of Vanderwaltozyma polyspora Nup133 Beta-propeller domain

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.2	298	Protein (10 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol, 5mM DTT), Reservoir (100mM Hepes pH 8.2, 10% PEG 3350, 100mM Ammonium Sulfate), Cryoprotection (30% Glycerol), VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.172	α = 90
b = 133.843	β = 90
c = 136.775	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	CCD	RAYONIX MX225HE	MIRRORS	2008-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97929	APS	31-ID

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	40	99.7	0.189	14.2	14.6		20381			88.3

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)
1	3	3.18	98.6		0.02542	1.2	13.9	3224

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	3	40	20310	1042	99.42	0.2175	0.2149	0.2249	0.2677	0.2759	RANDOM	101.079

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]
-5.48			2.52		2.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.793
r_dihedral_angle_4_deg	17.912
r_dihedral_angle_3_deg	15.698
r_dihedral_angle_1_deg	8.611
r_mcangle_it	3.017
r_mcbond_it	1.75
r_mcbond_other	1.75
r_angle_refined_deg	1.33
r_angle_other_deg	0.898
r_chiral_restr	0.074
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6097
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
Aimless	data scaling
PHENIX	phasing