3DA5

Crystal Structure of Piwi/Argonaute/Zwille(PAZ) domain from Thermococcus thioreducens

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1U04	PDB ENTRY 1U04

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	298	Dioxane, PEG8000, pH 8.5, vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.392	α = 90
b = 60.896	β = 90
c = 66.447	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	MARMOSAIC 300 mm CCD		2008-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.94	44.9	81.1	0.046	0.046	30.7	4.9		14536	1.7	3	32.7

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)
	1.94	2.01	59.4		0.32	0.32	3.23	3.7	1048

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1U04	1.94	44.9	17886	14511	730	81.13	0.218	0.216	0.267	RANDOM	34.363

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]
0.32			0.7		-1.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.248
r_dihedral_angle_4_deg	22.26
r_dihedral_angle_3_deg	15.9
r_dihedral_angle_1_deg	8.183
r_scangle_it	4.419
r_scbond_it	2.944
r_mcangle_it	2.276
r_angle_refined_deg	1.772
r_mcbond_it	1.459
r_angle_other_deg	0.991
r_mcbond_other	0.318
r_symmetry_hbond_refined	0.273
r_symmetry_vdw_other	0.25
r_symmetry_vdw_refined	0.24
r_nbd_refined	0.238
r_nbd_other	0.199
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.122
r_chiral_restr	0.115
r_nbtor_other	0.09
r_bond_refined_d	0.021
r_xyhbond_nbd_other	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2016
Nucleic Acid Atoms
Solvent Atoms	21
Heterogen Atoms

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling