Experiment: 3DV3

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP			VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
3.49	64.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.596	α = 90
b = 81.596	β = 90
c = 129.966	γ = 120

Symmetry
Space Group	P 62

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	MAR CCD 165 mm			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-BM		APS	17-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.25	100	99.2	0.049	12.2	7.6		23200

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.33	100		0.777		6.7	2328

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.3	47.83	21515	1103	99.18	0.184	0.182	0.221	RANDOM	55.39

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]
0.55	0.28		0.55		-0.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.638
r_dihedral_angle_4_deg	25.947
r_dihedral_angle_3_deg	19.921
r_dihedral_angle_1_deg	10.568
r_scangle_it	3.973
r_scbond_it	2.574
r_angle_refined_deg	1.9
r_mcangle_it	1.399
r_mcbond_it	0.878
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.638
r_dihedral_angle_4_deg	25.947
r_dihedral_angle_3_deg	19.921
r_dihedral_angle_1_deg	10.568
r_scangle_it	3.973
r_scbond_it	2.574
r_angle_refined_deg	1.9
r_mcangle_it	1.399
r_mcbond_it	0.878
r_nbtor_refined	0.304
r_nbd_refined	0.214
r_symmetry_vdw_refined	0.19
r_xyhbond_nbd_refined	0.18
r_chiral_restr	0.149
r_metal_ion_refined	0.123
r_symmetry_hbond_refined	0.122
r_bond_refined_d	0.022
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2255
Nucleic Acid Atoms
Solvent Atoms	86
Heterogen Atoms	67

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.