Experiment: 6W29

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GZ3	1GZ3, 3WJA, 1GQ2
experimental model	PDB	3WJA	1GZ3, 3WJA, 1GQ2
experimental model	PDB	1GQ2	1GZ3, 3WJA, 1GQ2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.1 M HEPES, 1.2-1.4 M Na3-Citrate

Crystal Properties
Matthews coefficient	Solvent content
2.56	52.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.519	α = 90
b = 73.519	β = 90
c = 233.713	γ = 90

Symmetry
Space Group	P 43 21 2

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 2M		2018-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.459	LNLS	W01B-MX2

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	2.14	47.54	99.9	0.13	0.136	0.04	0.998	13	11.1		36499

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	2.14	2.2	98.8		1.054	1.18	0.509	0.53		4.8

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	MOLECULAR REPLACEMENT	FREE R-VALUE	1GZ3, 3WJA, 1GQ2	2.14	47.54	34556	1840	99.84	0.2076	0.2059	0.2388	RANDOM	40.258

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]
1.45			1.45		-2.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.714
r_dihedral_angle_4_deg	18.915
r_dihedral_angle_3_deg	16.477
r_dihedral_angle_1_deg	6.732
r_angle_refined_deg	1.665
r_angle_other_deg	1.323
r_chiral_restr	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.714
r_dihedral_angle_4_deg	18.915
r_dihedral_angle_3_deg	16.477
r_dihedral_angle_1_deg	6.732
r_angle_refined_deg	1.665
r_angle_other_deg	1.323
r_chiral_restr	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4268
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms	61

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
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 R01GM133198.