Experiment: 6DUB

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	30% PEG2000, 0.1 M potassium thiocyanate

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.359	α = 90
b = 44.359	β = 90
c = 262.058	γ = 90

Symmetry
Space Group	P 43

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	RAYONIX MX-300		2016-01-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	31.14	96	0.074	0.081	0.032	0.998	11	6.1		150535

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.22	93.2		0.973	1.056	0.404	0.675		6.6	7191

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	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 5E1D	1.2	31.1	145394	4983	95.91	0.1548	0.154	0.1778	16.091

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]
-0.35			-0.35		0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.412
r_sphericity_free	18.025
r_dihedral_angle_4_deg	12.089
r_dihedral_angle_3_deg	11.493
r_sphericity_bonded	8.282
r_dihedral_angle_1_deg	6.176
r_mcangle_it	2.706
r_rigid_bond_restr	2.7
r_mcbond_it	2.024
r_mcbond_other	2.024

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.412
r_sphericity_free	18.025
r_dihedral_angle_4_deg	12.089
r_dihedral_angle_3_deg	11.493
r_sphericity_bonded	8.282
r_dihedral_angle_1_deg	6.176
r_mcangle_it	2.706
r_rigid_bond_restr	2.7
r_mcbond_it	2.024
r_mcbond_other	2.024
r_angle_refined_deg	1.823
r_angle_other_deg	0.921
r_chiral_restr	0.12
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3509
Nucleic Acid Atoms
Solvent Atoms	314
Heterogen Atoms	154

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	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 R01GM133198.