3FMP | pdb_00003fmp

Crystal structure of the nucleoporin Nup214 in complex with the DEAD-box helicase Ddx19

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3FMO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9.5	298	PEG 3000, CHES buffer, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.369	α = 90
b = 112.915	β = 89.86
c = 142.573	γ = 90

Symmetry
Space Group	P 1 21 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 315		2008-05-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	0.9795	ALS	8.2.1

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	3.2	50	91.3	0.113	14.3	6.8	32548	29717		-3

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	3.2	3.31	70.9		0.395	3.6	5.9	3249

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	3FMO	3.19	50	30998	28125	1504	90.73	0.25114	0.24938	0.25	0.28317	0.28	RANDOM	72.611

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]
16.88		0.93	-3.14		-13.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.135
r_dihedral_angle_3_deg	18.342
r_dihedral_angle_4_deg	16.856
r_dihedral_angle_1_deg	7.528
r_angle_refined_deg	1.471
r_scangle_it	1.047
r_angle_other_deg	0.899
r_scbond_it	0.688
r_mcangle_it	0.411
r_mcbond_it	0.308
r_symmetry_vdw_other	0.269
r_nbd_refined	0.229
r_nbd_other	0.201
r_symmetry_vdw_refined	0.197
r_nbtor_refined	0.19
r_xyhbond_nbd_refined	0.167
r_symmetry_hbond_refined	0.151
r_nbtor_other	0.091
r_chiral_restr	0.08
r_mcbond_other	0.069
r_xyhbond_nbd_other	0.026
r_bond_refined_d	0.013
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10162
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	54

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling