29HO | pdb_000029ho

Ternary complex of VCB, Baz2B-BD with compound 8

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4XUB
experimental model	PDB	8P0F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	100 mM Na-cacodylate pH 6.5, 170-250 mM Ca(OAc)2, 17-20% PEG8k

Crystal Properties
Matthews coefficient	Solvent content
3.12	60.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.65	α = 90
b = 73.355	β = 90
c = 149.531	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 EIGER2 X 16M		2025-02-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2.45	74.77	99.92	0.06154	0.0644	0.01836	0.966	15.87	13		25239			84.04

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	2.45	2.54	99.88		2.206	2.292	0.6189	0.855		13.5

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	2.45	74.766	25236	1375	99.956	0.233	0.2308	0.2349	0.2756	0.2868	114.056

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]
-3.511			1.199		2.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.568
r_dihedral_angle_6_deg	13.208
r_lrange_it	11.237
r_lrange_other	11.237
r_scangle_it	8.679
r_scangle_other	8.677
r_dihedral_angle_2_deg	8.544
r_dihedral_angle_1_deg	7.96
r_mcangle_it	7.276
r_mcangle_other	7.274
r_scbond_it	5.876
r_scbond_other	5.875
r_mcbond_it	4.802
r_mcbond_other	4.801
r_angle_refined_deg	1.579
r_angle_other_deg	0.666
r_nbd_refined	0.183
r_nbtor_refined	0.16
r_symmetry_nbd_other	0.145
r_xyhbond_nbd_refined	0.127
r_symmetry_nbd_refined	0.106
r_nbd_other	0.106
r_symmetry_xyhbond_nbd_refined	0.086
r_chiral_restr	0.079
r_symmetry_nbtor_other	0.069
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3737
Nucleic Acid Atoms
Solvent Atoms	40
Heterogen Atoms	89

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data collection
Aimless	data scaling
PHASER	phasing