Experiment: 3BK9

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NW7	PDB ENTRY 2nw7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.3	293	100mM Mes (pH 6.3), 10-12% (wt/vol) PEG 4000, 60mM MnCl2, 10mM sodium dithionite, 2mM L-Trp, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.222	α = 90
b = 117.606	β = 95.73
c = 139.283	γ = 90

Symmetry
Space Group	P 1 21 1

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	MAR CCD 165 mm		2007-01-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX10.1	1.381	SRS	PX10.1

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	2.15	59.66	96.9	0.1	9.5	2.4	312593	131764

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)
	2.15	2.27	91.7		0.474	2.5	2.3	18137

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 2nw7	2.15	54.13	125104	6624	96.73	0.2047	0.20047	0.2005	0.28457	0.2809	RANDOM	23.189

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]
1.37		0.17	-1.05		-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.948
r_dihedral_angle_4_deg	23.088
r_dihedral_angle_3_deg	19.023
r_dihedral_angle_1_deg	7.554
r_scangle_it	5.064
r_scbond_it	3.531
r_angle_refined_deg	2.346
r_mcangle_it	1.994
r_mcbond_it	1.315
r_symmetry_hbond_refined	0.443

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.948
r_dihedral_angle_4_deg	23.088
r_dihedral_angle_3_deg	19.023
r_dihedral_angle_1_deg	7.554
r_scangle_it	5.064
r_scbond_it	3.531
r_angle_refined_deg	2.346
r_mcangle_it	1.994
r_mcbond_it	1.315
r_symmetry_hbond_refined	0.443
r_xyhbond_nbd_refined	0.371
r_nbtor_refined	0.308
r_nbd_refined	0.227
r_symmetry_vdw_refined	0.224
r_chiral_restr	0.171
r_bond_refined_d	0.028
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17638
Nucleic Acid Atoms
Solvent Atoms	1016
Heterogen Atoms	419

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

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.