Experiment: 6V23

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	298	0.1 M magnesium formate and 16% (w/v) PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.028	α = 90
b = 71.192	β = 90
c = 130.03	γ = 90

Symmetry
Space Group	I 2 2 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 EIGER X 4M	X-ray mirrors VariMax HF	2018-05-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.75	40	95.3	0.046	0.05	0.02	19	5.8		27916

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	1.75	1.78	70.1		0.489	0.591	0.325	0.678		2.8

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	THROUGHOUT	3eca	1.75	24.44	26294	1396	94.35	0.185	0.182	0.2413	RANDOM	32.74

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]
-0.23			0.14		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.946
r_dihedral_angle_4_deg	14.183
r_dihedral_angle_3_deg	13.964
r_dihedral_angle_1_deg	7.438
r_angle_refined_deg	2.296
r_angle_other_deg	1.586
r_chiral_restr	0.116
r_bond_refined_d	0.019
r_gen_planes_refined	0.015
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.946
r_dihedral_angle_4_deg	14.183
r_dihedral_angle_3_deg	13.964
r_dihedral_angle_1_deg	7.438
r_angle_refined_deg	2.296
r_angle_other_deg	1.586
r_chiral_restr	0.116
r_bond_refined_d	0.019
r_gen_planes_refined	0.015
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2357
Nucleic Acid Atoms
Solvent Atoms	236
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
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 R01GM157729.