Experiment: 5OGP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3PO6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	291	1.6 M sodium citrate 50 mM Tris-HCl pH 7.8.

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.835	α = 90
b = 41.231	β = 103.95
c = 72.395	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		2014-08-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

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	1.1	40.6	78.5	0.035	0.041	0.999	17.89	3.444		76291		-3	15.201

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	1.1	1.17	24.7		0.403	0.54	0.779	1.86	2.192

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	FOURIER SYNTHESIS	THROUGHOUT	3PO6	1.1	40.6	74765	1526	78.53	0.1249	0.1244	0.13	0.1499	0.15	RANDOM	16.139

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]
-0.37		-0.11	-0.01		0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.156
r_sphericity_free	18.969
r_dihedral_angle_4_deg	18.659
r_dihedral_angle_3_deg	12.505
r_sphericity_bonded	11.005
r_dihedral_angle_1_deg	7.709
r_rigid_bond_restr	3.606
r_angle_other_deg	2.405
r_angle_refined_deg	1.732
r_chiral_restr	0.112

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.156
r_sphericity_free	18.969
r_dihedral_angle_4_deg	18.659
r_dihedral_angle_3_deg	12.505
r_sphericity_bonded	11.005
r_dihedral_angle_1_deg	7.709
r_rigid_bond_restr	3.606
r_angle_other_deg	2.405
r_angle_refined_deg	1.732
r_chiral_restr	0.112
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_gen_planes_other	0.006
r_bond_other_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2032
Nucleic Acid Atoms
Solvent Atoms	362
Heterogen Atoms	59

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
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.