Experiment: 6YZR

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4MDG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	291	1.6 M sodium citrate, 50 mM Tris-H2SO4

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.216	α = 90
b = 41.374	β = 104.33
c = 71.909	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 PILATUS3 6M		2016-11-15	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	1.2	40.9	98.5	0.047	0.054	0.999	15.24	4.647		74406			16.778

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	1.2	1.27	98.3		0.521	0.588	0.814	2.48	4.594

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	4MDG	1.2	40.9	73358	1089	98.58	0.1331	0.1326	0.1353	0.162	0.161	RANDOM	17.516

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]
0.18		0.07	-0.8		0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.164
r_dihedral_angle_4_deg	22.536
r_sphericity_free	22.396
r_sphericity_bonded	11.805
r_dihedral_angle_3_deg	11.374
r_rigid_bond_restr	9.773
r_dihedral_angle_1_deg	6.691
r_angle_other_deg	5.671
r_angle_refined_deg	1.82
r_chiral_restr	0.117

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.164
r_dihedral_angle_4_deg	22.536
r_sphericity_free	22.396
r_sphericity_bonded	11.805
r_dihedral_angle_3_deg	11.374
r_rigid_bond_restr	9.773
r_dihedral_angle_1_deg	6.691
r_angle_other_deg	5.671
r_angle_refined_deg	1.82
r_chiral_restr	0.117
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_bond_other_d	0.009
r_gen_planes_other	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2024
Nucleic Acid Atoms
Solvent Atoms	308
Heterogen Atoms	58

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.