Experiment: 3BD6

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PRJ	PDB ENTRY 2PRJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	SMALL TUBES	6.7	289	10mM Bes buffer, 3mM DDT, pH6.7, SMALL TUBES, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.62	α = 90
b = 128.62	β = 90
c = 116.379	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	CCD	MAR CCD 165 mm		2005-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.81	EMBL/DESY, HAMBURG	X11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2	30	98.5	0.047	18.6	4.9	65282	65282		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.03	98.1		0.435	4.5	4.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 2PRJ	2	21.58	61937	3311	98.48	0.19092	0.19015	0.20515	RANDOM	34.177

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]
0.85			0.85		-1.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.959
r_dihedral_angle_4_deg	17.531
r_dihedral_angle_3_deg	15.174
r_dihedral_angle_1_deg	5.025
r_scangle_it	1.969
r_scbond_it	1.205
r_angle_refined_deg	1.023
r_mcangle_it	0.941
r_mcbond_it	0.547
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.959
r_dihedral_angle_4_deg	17.531
r_dihedral_angle_3_deg	15.174
r_dihedral_angle_1_deg	5.025
r_scangle_it	1.969
r_scbond_it	1.205
r_angle_refined_deg	1.023
r_mcangle_it	0.941
r_mcbond_it	0.547
r_nbtor_refined	0.302
r_nbd_refined	0.18
r_symmetry_vdw_refined	0.164
r_xyhbond_nbd_refined	0.101
r_chiral_restr	0.074
r_symmetry_hbond_refined	0.066
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6638
Nucleic Acid Atoms
Solvent Atoms	263
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	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 R01GM133198.