2CI9 | pdb_00002ci9

Nck1 SH2-domain in complex with a dodecaphosphopeptide from EPEC protein Tir

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		NCK1-APO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5		TECHNIQUE: HANGING-DROP, VAPOR-DIFFUSION PROTEIN CONCENTRATION: 8MG/ML PROTEIN:LIGAND = 1:1.1 RESERVOIRE: 2.4M (NH4)2HPO4, 0.1M TRIS, PH 8.5 CRYOCONDITIONS: 50% MPD

Crystal Properties
Matthews coefficient	Solvent content
2.26	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.092	α = 90
b = 60.518	β = 90
c = 65.061	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	MARRESEARCH	2 AU-COATED X-RAY MIRRORS	2004-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6		MPG/DESY, HAMBURG	BW6

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	1.4	30	96.4	0.04	28.1	4		38419

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	1.4	1.42	88		0.31	4.2	3.7

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	NCK1-APO	1.5	28.02	28813	1532	85.4	0.198	0.196	0.2	0.235	0.24	RANDOM	11.68

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]
0.05			-0.09		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.809
r_dihedral_angle_4_deg	22.083
r_dihedral_angle_3_deg	12.252
r_dihedral_angle_1_deg	4.672
r_scangle_it	2.548
r_mcangle_it	2.473
r_angle_refined_deg	2.171
r_scbond_it	1.857
r_mcbond_it	1.703
r_angle_other_deg	1.572
r_nbd_refined	0.203
r_nbtor_refined	0.17
r_symmetry_vdw_other	0.169
r_nbd_other	0.16
r_symmetry_hbond_refined	0.137
r_symmetry_vdw_refined	0.13
r_xyhbond_nbd_refined	0.122
r_chiral_restr	0.111
r_nbtor_other	0.076
r_bond_refined_d	0.012
r_bond_other_d	0.007
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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	1825
Nucleic Acid Atoms
Solvent Atoms	255
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing