8G3X

MBP-Mcl1 in complex with ligand 32

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4WMS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	285	20.5% (w/v) PEG3350, 0.11M Mg formate

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.4	α = 90
b = 137.378	β = 90
c = 38.491	γ = 90

Symmetry
Space Group	P 21 21 2

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		2021-09-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.0000	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.46	80.53	99.6	0.054	0.057	0.02	0.998	16.4	8.3		92781

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.46	1.48	98.3		1.226	1.304	0.438	0.795	1.3	8.5

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.46	80.53	87951	4829	99.55	0.18356	0.18232	0.2059	RANDOM	34.337

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]
1.06			-1.55		0.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.038
r_dihedral_angle_4_deg	16.647
r_dihedral_angle_3_deg	12.172
r_long_range_B_refined	5.738
r_long_range_B_other	5.462
r_dihedral_angle_1_deg	5.2
r_scangle_other	2.92
r_mcangle_it	1.93
r_mcangle_other	1.93
r_scbond_it	1.869
r_scbond_other	1.867
r_angle_refined_deg	1.367
r_mcbond_it	1.301
r_mcbond_other	1.301
r_angle_other_deg	0.943
r_chiral_restr	0.081
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4042
Nucleic Acid Atoms
Solvent Atoms	557
Heterogen Atoms	127

Software

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