Experiment: 7MDS

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1 M HEPES pH 7.5, 0.1 M NaCl, 1.4 M (NH4)2SO4

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.47	α = 90
b = 94.47	β = 90
c = 181.41	γ = 90

Symmetry
Space Group	P 41 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	100	PIXEL	DECTRIS EIGER X 16M		2019-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.29	20	99.4	0.099	0.1	0.999	27.85	13.1		37390			34.68

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.29	2.43	0.966		0.391	0.407	0.978	7.92	12.8

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6VVI	2.295	20	37242	1071	99.143	0.184	0.183	0.2256	44.684

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]
0.887			0.887		-1.774

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.123
r_dihedral_angle_4_deg	17.313
r_dihedral_angle_3_deg	14.943
r_lrange_it	9.879
r_scangle_it	8.89
r_dihedral_angle_1_deg	6.724
r_scbond_it	6.13
r_mcangle_it	4.429
r_mcbond_it	3.424
r_angle_refined_deg	1.415

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.123
r_dihedral_angle_4_deg	17.313
r_dihedral_angle_3_deg	14.943
r_lrange_it	9.879
r_scangle_it	8.89
r_dihedral_angle_1_deg	6.724
r_scbond_it	6.13
r_mcangle_it	4.429
r_mcbond_it	3.424
r_angle_refined_deg	1.415
r_nbtor_refined	0.313
r_symmetry_nbd_refined	0.276
r_nbd_refined	0.207
r_symmetry_xyhbond_nbd_refined	0.2
r_xyhbond_nbd_refined	0.113
r_chiral_restr	0.107
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4796
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms	83

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
Auto-Rickshaw	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.