6PI7 | pdb_00006pi7

Crystal structure of the TDRD2 extended Tudor domain in complex with an antibody fragment and the PIWIL1 peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3PNW	pdb entry 3pnw

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	20.0% (V/V) PEG 3350, 0.2 M tri- lithium citrate

Crystal Properties
Matthews coefficient	Solvent content
3.46	64.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 148.099	α = 90
b = 148.099	β = 90
c = 168.026	γ = 120

Symmetry
Space Group	P 63

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		2012-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97934	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	48.48	99.8	0.106	0.111	0.033	0.998	16.6	11.3		51311

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.89	100		1.316	1.377	0.404	0.565		11.6	4414

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 3pnw	2.8	48.48	48719	2561	99.83	0.1912	0.1904	0.1906	0.2062	0.2043	79.148

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]
-18.85			-18.85		37.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.289
r_dihedral_angle_3_deg	14.369
r_dihedral_angle_4_deg	14.349
r_dihedral_angle_1_deg	6.948
r_mcangle_it	1.365
r_angle_refined_deg	1.28
r_angle_other_deg	1.199
r_mcbond_it	0.805
r_mcbond_other	0.805
r_chiral_restr	0.04
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8993
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	5

Software

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