Experiment: 2OMV

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
2.19	43.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.373	α = 90
b = 87.377	β = 90
c = 110.955	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	BESSY BEAMLINE 14.1	0.95	BESSY	14.1

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	1.9	50	97.3	0.085	7.9	4.9		42046

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	1.9	1.97	85.8		0.422		4.2	3636

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	1.9	50	41988	2136	97.21	0.157	0.153	0.16	0.219	RANDOM	20.47

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]
-1.03			1.63		-0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.371
r_dihedral_angle_3_deg	12.395
r_dihedral_angle_4_deg	12.178
r_dihedral_angle_1_deg	5.002
r_scangle_it	3.606
r_mcangle_it	2.753
r_scbond_it	2.653
r_mcbond_it	2.193
r_angle_refined_deg	1.696
r_nbtor_refined	0.285

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.371
r_dihedral_angle_3_deg	12.395
r_dihedral_angle_4_deg	12.178
r_dihedral_angle_1_deg	5.002
r_scangle_it	3.606
r_mcangle_it	2.753
r_scbond_it	2.653
r_mcbond_it	2.193
r_angle_refined_deg	1.696
r_nbtor_refined	0.285
r_nbd_refined	0.18
r_symmetry_vdw_refined	0.169
r_symmetry_hbond_refined	0.139
r_xyhbond_nbd_refined	0.12
r_chiral_restr	0.079
r_bond_refined_d	0.021
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4293
Nucleic Acid Atoms
Solvent Atoms	837
Heterogen Atoms	4

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.