Experiment: 6TMD

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.7	294	0.2 M ammonium acetate, 0.1 M Bis-tris pH 5.7, 31% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.778	α = 90
b = 45.659	β = 100.38
c = 51.073	γ = 90

Symmetry
Space Group	C 1 2 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	PIXEL	DECTRIS PILATUS 6M-F		2019-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.915870	Diamond	I04-1

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	1.5	47.15	99.2	0.056	0.067	0.036	0.999	10.3	3.4		35000

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	1.5	1.521	99.9		2.239	2.674	1.45	0.329	0.5	3.2

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	4hbd	1.5	47.15	32838	1674	97.8	0.1788	0.1768	0.2203	RANDOM	27.083

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]
2.48		0.5	-1.49		-1.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.505
r_dihedral_angle_4_deg	22.156
r_dihedral_angle_3_deg	14.114
r_dihedral_angle_1_deg	5.102
r_angle_refined_deg	1.565
r_angle_other_deg	1.472
r_chiral_restr	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.505
r_dihedral_angle_4_deg	22.156
r_dihedral_angle_3_deg	14.114
r_dihedral_angle_1_deg	5.102
r_angle_refined_deg	1.565
r_angle_other_deg	1.472
r_chiral_restr	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1832
Nucleic Acid Atoms
Solvent Atoms	186
Heterogen Atoms	38

Software

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