7O92 | pdb_00007o92

hypothetical protein UY81_C0065G0003 residues 18-54 from Candidatus Giovannonibacteria bacterium fused to GCN4 adaptors

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YNY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	0.1M sodium acetate (pH 4.6), 2M sodium formate

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.089	α = 90
b = 39.842	β = 103.36
c = 78.21	γ = 90

Symmetry
Space Group	P 1 21 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		2017-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.0	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.7	40	99.1	0.051	1	13.12	3.28		7604

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.86	96.7		0.61	0.9	1.67	3.15

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	2YNY	2.7	40	7043	572	99.48	0.2726	0.2694	0.27	0.3139	0.31	RANDOM	73.322

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]
4.1		-4.88	4.21		-5.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.061
r_dihedral_angle_3_deg	17.704
r_dihedral_angle_4_deg	6.1
r_dihedral_angle_1_deg	3.622
r_angle_refined_deg	0.922
r_angle_other_deg	0.907
r_chiral_restr	0.049
r_bond_refined_d	0.006
r_bond_other_d	0.003
r_gen_planes_refined	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.061
r_dihedral_angle_3_deg	17.704
r_dihedral_angle_4_deg	6.1
r_dihedral_angle_1_deg	3.622
r_angle_refined_deg	0.922
r_angle_other_deg	0.907
r_chiral_restr	0.049
r_bond_refined_d	0.006
r_bond_other_d	0.003
r_gen_planes_refined	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2128
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
MOLREP	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 R01GM157729.