Experiment: 8YVH

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291.15	PEG3350, magnesium chloride, Tris-Hcl pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.37

Symmetry
Space Group	P 1 21 1

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	Bruker PHOTON III		2023-07-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	LIQUID ANODE	BRUKER METALJET	1.34138

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	35.09	98.4	0.0638	13.36	3.99		36140

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	2.03	84.2		0.1661	2.08	2.08

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.1	35.09	29740	1596	99.35	0.17061	0.16687	0.1753	0.2414	0.2475	RANDOM	22.384

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]
1.54		-0.41	0.33		-1.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.845
r_dihedral_angle_3_deg	15.556
r_dihedral_angle_4_deg	13.943
r_dihedral_angle_1_deg	6.042
r_long_range_B_refined	5.084
r_long_range_B_other	5.009
r_scangle_other	3.326
r_mcangle_it	2.306
r_mcangle_other	2.305
r_scbond_it	2.192

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.845
r_dihedral_angle_3_deg	15.556
r_dihedral_angle_4_deg	13.943
r_dihedral_angle_1_deg	6.042
r_long_range_B_refined	5.084
r_long_range_B_other	5.009
r_scangle_other	3.326
r_mcangle_it	2.306
r_mcangle_other	2.305
r_scbond_it	2.192
r_scbond_other	2.192
r_angle_refined_deg	1.58
r_mcbond_other	1.526
r_mcbond_it	1.525
r_angle_other_deg	1.327
r_chiral_restr	0.071
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded