9MZA | pdb_00009mza

Chemically Hijacked BCL6-TCIP3-p300 Complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6CQ1
experimental model	PDB	5BT3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	0.15 M DL-Malic acid pH 7.0, PEG 3,350 20%

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.388	α = 90
b = 94.79	β = 90
c = 97.616	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 PILATUS 6M	Rh coated flat bent M0, toroidal focusing post-monochromator M1	2023-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97946	SSRL	BL9-2

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	2.01	60.16	99.2	0.122	6.7	5.4		47662

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	2.01	2.06	98.6		1.764

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	2.1	60	41640	2021	98.933	0.22	0.2175	0.2447	0.2765	0.2916	47.937

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]
6.775			-4.123		-2.652

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.833
r_dihedral_angle_3_deg	16.131
r_dihedral_angle_6_deg	14.339
r_lrange_it	11.36
r_lrange_other	11.347
r_scangle_it	8.556
r_scangle_other	8.555
r_mcangle_it	6.698
r_mcangle_other	6.698
r_dihedral_angle_1_deg	6.389
r_scbond_it	5.577
r_scbond_other	5.577
r_mcbond_it	4.667
r_mcbond_other	4.667
r_angle_refined_deg	1.709
r_angle_other_deg	0.57
r_nbd_refined	0.237
r_xyhbond_nbd_refined	0.23
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.193
r_nbd_other	0.178
r_symmetry_xyhbond_nbd_other	0.124
r_symmetry_xyhbond_nbd_refined	0.119
r_ncsr_local_group_2	0.1
r_symmetry_nbd_refined	0.085
r_ncsr_local_group_1	0.081
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.079
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3884
Nucleic Acid Atoms
Solvent Atoms	428
Heterogen Atoms	162

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing