Experiment: 6BHD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		similar, nearly isomorphous crystal structure, to be published

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	291	25% PEG3350, 0.2 M sodium chloride, 0.1 M HEPES, 5% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.258	α = 90
b = 72.448	β = 104.84
c = 52.505	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	ADSC QUANTUM 315r		2013-08-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9686	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	1.25	41.57	99.8	0.05	0.059	0.03	0.999	15.1	3.7		74273

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	1.25	1.27	99.8		1.018	1.198	0.625	0.487		3.6	3645

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	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	similar, nearly isomorphous crystal structure, to be published	1.25	41.57	70524	3722	99.8	0.1492	0.1474	0.1829	16.006

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]
-0.17		-0.06	0.32		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.886
r_sphericity_free	19.119
r_dihedral_angle_4_deg	17.305
r_dihedral_angle_3_deg	12.186
r_sphericity_bonded	8.964
r_dihedral_angle_1_deg	6.949
r_mcangle_it	4.028
r_mcbond_it	3.228
r_mcbond_other	3.224
r_rigid_bond_restr	2.955

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.886
r_sphericity_free	19.119
r_dihedral_angle_4_deg	17.305
r_dihedral_angle_3_deg	12.186
r_sphericity_bonded	8.964
r_dihedral_angle_1_deg	6.949
r_mcangle_it	4.028
r_mcbond_it	3.228
r_mcbond_other	3.224
r_rigid_bond_restr	2.955
r_angle_refined_deg	1.937
r_angle_other_deg	1.106
r_chiral_restr	0.127
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1805
Nucleic Acid Atoms
Solvent Atoms	203
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	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.