3FHC | pdb_00003fhc

Crystal structure of human Dbp5 in complex with Nup214

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OIT	PDB ENTRIES 2OIT and 3FHT
experimental model	PDB	3FHT	PDB ENTRIES 2OIT and 3FHT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	50mM MES pH 6.0, 900mM Na citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.22	70.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.409	α = 90
b = 134.707	β = 90
c = 152.845	γ = 90

Symmetry
Space Group	I 2 2 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	MARRESEARCH		2008-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.99988	SLS	X06SA

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	2.8	47.7	100	0.138	11.59	14.13	30169	30169		3.3	45.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	3	100		0.364	0.36	3.31	13.6	5545

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	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 ENTRIES 2OIT and 3FHT	2.8	47.65	3.31	30169	30169	1509	100	0.22	0.218	0.22	0.26	0.26	RANDOM	42.137

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]
-1.45			3.59		-2.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.541
r_dihedral_angle_4_deg	18.878
r_dihedral_angle_3_deg	17.313
r_dihedral_angle_1_deg	6.687
r_scangle_it	2.55
r_scbond_it	1.414
r_angle_refined_deg	1.341
r_mcangle_it	1.183
r_mcbond_it	0.622
r_chiral_restr	0.083
r_bond_refined_d	0.011
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4736
Nucleic Acid Atoms
Solvent Atoms	86
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing