3KFO | pdb_00003kfo

Crystal structure of the C-terminal domain from the nuclear pore complex component NUP133 from Saccharomyces cerevisiae

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	20% PEG 3350, 200mM Potassium Thiocyanate, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.433	α = 90
b = 52.678	β = 90
c = 76.674	γ = 90

Symmetry
Space Group	P 21 21 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		2009-07-31	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 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	1.9	31	99.7	0.121	10.6	7.7		15683			19.5

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	1.9	2	100		0.414	4.6	7.8	2236

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	1.9	23	15628	811	99.67	0.193	0.191	0.2	0.245	0.25	RANDOM	23.975

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]
0.01			-0.02		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.694
r_dihedral_angle_3_deg	13.929
r_dihedral_angle_4_deg	13.775
r_dihedral_angle_1_deg	5.34
r_scangle_it	4.728
r_scbond_it	3.172
r_mcangle_it	1.991
r_angle_refined_deg	1.635
r_mcbond_it	1.282
r_angle_other_deg	1.001
r_mcbond_other	0.3
r_symmetry_vdw_refined	0.28
r_nbd_refined	0.226
r_nbd_other	0.193
r_nbtor_refined	0.187
r_symmetry_vdw_other	0.183
r_xyhbond_nbd_refined	0.164
r_symmetry_hbond_refined	0.149
r_chiral_restr	0.099
r_nbtor_other	0.092
r_bond_refined_d	0.018
r_bond_other_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1669
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing
SHELXD	phasing
SHELXE	model building