2WJY | pdb_00002wjy

Crystal structure of the complex between human nonsense mediated decay factors UPF1 and UPF2 Orthorhombic form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GK7	PDB ENTRIES 2GK7, 2IYK
experimental model	PDB	2IYK	PDB ENTRIES 2GK7, 2IYK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6		1.6M AMMONIUM SULPHATE, 100 MM MES PH 6, 10% DIOXANE

Crystal Properties
Matthews coefficient	Solvent content
3.23	62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.91	α = 90
b = 129.14	β = 90
c = 311.27	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	ADSC CCD		2008-03-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

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	2.5	30	98.4	0.11	11.2	3.71		45136

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	2.5	2.6	98		0.77	1.9	3.78

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 2GK7, 2IYK	2.5	46.52	42869	2266	98.38	0.19777	0.19552	0.2	0.2403	0.25	RANDOM	45.9

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]
-0.72			0.35		0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.747
r_dihedral_angle_4_deg	19.173
r_dihedral_angle_3_deg	17.786
r_dihedral_angle_1_deg	6.408
r_scangle_it	3.083
r_scbond_it	1.827
r_angle_refined_deg	1.386
r_mcangle_it	1.139
r_mcbond_it	0.575
r_chiral_restr	0.093
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6107
Nucleic Acid Atoms
Solvent Atoms	254
Heterogen Atoms	43

Software

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