Experiment: 8VLH

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.1 M Bis-Tris propane pH 10, 0.25 M strontium chloride, 0.01 M ammonium sulfate, and 25% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 173.11	α = 90
b = 60.575	β = 97.92
c = 53.588	γ = 90

Symmetry
Space Group	C 1 2 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 PILATUS 200K		2020-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5419

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	2.4	48.2	97	0.063	0.077	0.996	12.2	2.8		20953

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	2.4	2.49			0.319	0.429	0.841	2.3

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4L58 and 1W4S	2.403	48.2	20951	1062	96.852	0.233	0.2298	0.2302	0.2845	0.2836	43.147

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]
2.487		0.021	-0.082		-2.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.737
r_dihedral_angle_3_deg	15.32
r_dihedral_angle_4_deg	11.906
r_dihedral_angle_1_deg	6.001
r_angle_refined_deg	0.736
r_nbtor_refined	0.303
r_symmetry_nbd_refined	0.184
r_nbd_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.129
r_xyhbond_nbd_refined	0.113

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.737
r_dihedral_angle_3_deg	15.32
r_dihedral_angle_4_deg	11.906
r_dihedral_angle_1_deg	6.001
r_angle_refined_deg	0.736
r_nbtor_refined	0.303
r_symmetry_nbd_refined	0.184
r_nbd_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.129
r_xyhbond_nbd_refined	0.113
r_chiral_restr	0.064
r_bond_refined_d	0.002
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4101
Nucleic Acid Atoms
Solvent Atoms	145
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MrBUMP	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.