9PQ5 | pdb_00009pq5

MBP-Mcl1 in complex with ligand 8

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		previously solved structure of MBP-Mcl-1 fusion protein was used as a search model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	285	19% (w/v) PEG3350, 0.17M Magnesium formate

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.139	α = 90
b = 137.018	β = 90
c = 38.524	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 EIGER X 16M		2019-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.9999	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.28	80.34	99.5	0.032	1	19.96	5		135419

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.28	1.53	99.6		0.522		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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.28	80.34	128507	6912	99.55	0.15308	0.15092	0.1605	0.19456	0.1989	RANDOM	24.742

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]
0.15			-0.4		0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.266
r_sphericity_free	21.337
r_dihedral_angle_4_deg	16.979
r_dihedral_angle_3_deg	12.48
r_rigid_bond_restr	9.432
r_sphericity_bonded	8.234
r_dihedral_angle_1_deg	5.601
r_scbond_it	4.143
r_scbond_other	4.143
r_scangle_other	3.933
r_long_range_B_refined	3.922
r_long_range_B_other	3.921
r_mcangle_other	3.1
r_mcangle_it	3.071
r_mcbond_it	2.83
r_mcbond_other	2.751
r_angle_refined_deg	1.826
r_angle_other_deg	1.461
r_chiral_restr	0.117
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_gen_planes_other	0.005
r_bond_other_d	0.003
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4042
Nucleic Acid Atoms
Solvent Atoms	690
Heterogen Atoms	69

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
REFMAC	phasing
PDB_EXTRACT	data extraction