Experiment: 6BDT

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	295.15	PEG 8000, MES, calcium chloride

Crystal Properties
Matthews coefficient	Solvent content
2	38.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.81	α = 90
b = 105.49	β = 90
c = 225.26	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	ADSC QUANTUM 210	Oxford Danfysik toroidal focusing mirror	2014-04-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	1.0781	NSLS	X6A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.3	50	97.9	0.21	0.997	11.22	14.2		62975

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.32	96.5		1.3	0.8	2.16	13.89

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	MOLECULAR REPLACEMENT	THROUGHOUT	1MDW	2.3	17.99	59691	3139	98.17	0.2236	0.2219	0.256	RANDOM	60.172

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]
3.13			-1.3		-1.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.373
r_dihedral_angle_4_deg	15.235
r_dihedral_angle_3_deg	13.999
r_dihedral_angle_1_deg	5.963
r_angle_refined_deg	1.35
r_angle_other_deg	1.218
r_chiral_restr	0.084
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.373
r_dihedral_angle_4_deg	15.235
r_dihedral_angle_3_deg	13.999
r_dihedral_angle_1_deg	5.963
r_angle_refined_deg	1.35
r_angle_other_deg	1.218
r_chiral_restr	0.084
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.006
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10374
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	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 R01GM133198.