3O6E | pdb_00003o6e

Crystal Structure of human Hiwi1 PAZ domain (residues 277-399) in complex with 14-mer RNA (12-bp + 2-nt overhang) containing 2'-OCH3 at its 3'-end

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3O7V	PDB ENTRY 3O7V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	277	1-5% PEG3350, 50 mM NaCl, 50 mM Na-acetate buffer, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.87	34.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.013	α = 90
b = 44.013	β = 90
c = 147.024	γ = 90

Symmetry
Space Group	P 41 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 QUANTUM 315	vertical focusing mirror	2009-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9792	NSLS	X29A

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	2.9	30	95.3	0.083	32.5	10.4		3451

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)
	2.9	3	72.3		0.209	4.8	6.2	245

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 ENTRY 3O7V	2.904	15	3384	305	95.27	0.2562	0.2515	0.25	0.3051	0.3	RANDOM	61.5548

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]
2.55			2.55		-5.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.208
r_dihedral_angle_3_deg	13.429
r_dihedral_angle_1_deg	4.211
r_dihedral_angle_4_deg	2.725
r_angle_refined_deg	0.842
r_scangle_it	0.522
r_scbond_it	0.338
r_mcangle_it	0.258
r_mcbond_it	0.131
r_chiral_restr	0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.208
r_dihedral_angle_3_deg	13.429
r_dihedral_angle_1_deg	4.211
r_dihedral_angle_4_deg	2.725
r_angle_refined_deg	0.842
r_scangle_it	0.522
r_scbond_it	0.338
r_mcangle_it	0.258
r_mcbond_it	0.131
r_chiral_restr	0.05
r_bond_refined_d	0.005
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	855
Nucleic Acid Atoms	293
Solvent Atoms	6
Heterogen Atoms

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.