Experiment: 2OMT

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O6S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	PEG 4000, CaCl2, Na-Acetate, Tris/MES, pH 6.0, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.24	α = 90
b = 88.47	β = 90
c = 110.49	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	MAR CCD 165 mm			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.81	EMBL/DESY, HAMBURG	X13

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	40	95.8	0.121	9.44	5		36174		-3	23.269

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)
1	2	2.1	91.5		0.37	3.9	3	4620

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	1O6S	2	40	36029	1800	96.5	0.199	0.194	0.2	0.283	0.28	RANDOM	18.242

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]
-0.8			0.77		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.236
r_dihedral_angle_4_deg	19.23
r_dihedral_angle_3_deg	17.76
r_dihedral_angle_1_deg	7.785
r_scangle_it	4.165
r_scbond_it	2.994
r_angle_refined_deg	2.129
r_mcangle_it	1.686
r_mcbond_it	1.109
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.236
r_dihedral_angle_4_deg	19.23
r_dihedral_angle_3_deg	17.76
r_dihedral_angle_1_deg	7.785
r_scangle_it	4.165
r_scbond_it	2.994
r_angle_refined_deg	2.129
r_mcangle_it	1.686
r_mcbond_it	1.109
r_nbtor_refined	0.309
r_metal_ion_refined	0.282
r_symmetry_hbond_refined	0.274
r_nbd_refined	0.242
r_xyhbond_nbd_refined	0.223
r_symmetry_vdw_refined	0.212
r_chiral_restr	0.14
r_bond_refined_d	0.023
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4310
Nucleic Acid Atoms
Solvent Atoms	598
Heterogen Atoms	2

Software

Software
Software Name	Purpose
XSCALE	data scaling
EPMR	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

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.