Experiment: 6Z04

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5OGP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	50 mM Tris pH=7.8 1.6 M Natrium Citrate

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.035	α = 90
b = 41.345	β = 103.98
c = 72.682	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		2016-09-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	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	1.05	40.79	97.8	0.069	0.082	0.997	7.9	3.258		111433			13.945

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	1.05	1.11	94.6		0.835	1.01	0.467	1.12	3.081

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	5OGP	1.05	40.79	109331	2101	97.86	0.1412	0.1408	0.1578	RANDOM	15.626

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]
-0.13		-0.03	-0.09		0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.733
r_dihedral_angle_4_deg	18.118
r_sphericity_free	13.778
r_dihedral_angle_3_deg	10.535
r_dihedral_angle_1_deg	6.997
r_sphericity_bonded	6.77
r_angle_other_deg	2.394
r_rigid_bond_restr	2.284
r_angle_refined_deg	1.629
r_chiral_restr	0.107

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.733
r_dihedral_angle_4_deg	18.118
r_sphericity_free	13.778
r_dihedral_angle_3_deg	10.535
r_dihedral_angle_1_deg	6.997
r_sphericity_bonded	6.77
r_angle_other_deg	2.394
r_rigid_bond_restr	2.284
r_angle_refined_deg	1.629
r_chiral_restr	0.107
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.007
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2010
Nucleic Acid Atoms
Solvent Atoms	286
Heterogen Atoms	20

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
FFT	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.