Experiment: 2OMU

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
2.43	49.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.01	α = 74.98
b = 54.273	β = 80.82
c = 68.643	γ = 67.36

Symmetry
Space Group	P 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	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	1.8	20	93.7	0.094	7.6			50001

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	1.8	1.86	74.9		0.623			3960

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1O6S	1.8	20	49998	2548	93.45	0.167	0.164	0.17	0.217	RANDOM	15.388

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]
0.33	0.77	-0.06	-0.75	-0.16	-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.416
r_dihedral_angle_3_deg	12.535
r_dihedral_angle_4_deg	11.985
r_dihedral_angle_1_deg	5.335
r_scangle_it	2.76
r_mcangle_it	2.178
r_scbond_it	1.918
r_angle_refined_deg	1.87
r_mcbond_it	1.647
r_nbtor_refined	0.279

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.416
r_dihedral_angle_3_deg	12.535
r_dihedral_angle_4_deg	11.985
r_dihedral_angle_1_deg	5.335
r_scangle_it	2.76
r_mcangle_it	2.178
r_scbond_it	1.918
r_angle_refined_deg	1.87
r_mcbond_it	1.647
r_nbtor_refined	0.279
r_nbd_refined	0.182
r_symmetry_vdw_refined	0.15
r_symmetry_hbond_refined	0.139
r_xyhbond_nbd_refined	0.125
r_chiral_restr	0.12
r_bond_refined_d	0.022
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4316
Nucleic Acid Atoms
Solvent Atoms	775
Heterogen Atoms	2

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

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.