9VVN | pdb_00009vvn

Crystal structure of computationally designed protein VTP-4

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.01M NiCl2, 0.1M Tris-HCl pH8.5, 20% w/v Polyethylene glycol Monomethyl ether 2,000

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.606	α = 90
b = 58.488	β = 90
c = 83.828	γ = 90

Symmetry
Space Group	P 21 21 21

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 16M		2024-11-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	0.999990	SPring-8	BL45XU

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	1.6	47.97	99.9	0.085	14.9	11		23836

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	1.6	1.63			0.996

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.6	47.967	23781	1169	99.828	0.21	0.2073	0.2188	0.2546	0.2645	24.626

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]
0.008			-0.218		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.136
r_dihedral_angle_3_deg	12.28
r_lrange_it	7.495
r_lrange_other	7.438
r_dihedral_angle_1_deg	6.13
r_scangle_it	5.814
r_scangle_other	5.811
r_dihedral_angle_2_deg	5.773
r_scbond_it	3.795
r_scbond_other	3.792
r_mcangle_other	3.49
r_mcangle_it	3.486
r_mcbond_it	2.527
r_mcbond_other	2.527
r_angle_refined_deg	2.003
r_angle_other_deg	0.625
r_symmetry_xyhbond_nbd_refined	0.265
r_symmetry_nbd_refined	0.218
r_nbd_refined	0.213
r_symmetry_nbd_other	0.201
r_xyhbond_nbd_refined	0.2
r_nbtor_refined	0.191
r_nbd_other	0.19
r_symmetry_nbtor_other	0.089
r_chiral_restr	0.085
r_symmetry_xyhbond_nbd_other	0.084
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1308
Nucleic Acid Atoms
Solvent Atoms	135
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing