9PW6 | pdb_00009pw6

Myeloid cell leukemia-1 (Mcl-1) complexed 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	4HW2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	25-30% PEG 3350, 0.1 M Bis-TRIS pH 6.5, 0.2 M MgCl2

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.613	α = 90
b = 87.678	β = 102.422
c = 50.348	γ = 90

Symmetry
Space Group	P 1 21 1

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		2016-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.9785	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.06	28.386	97.79	0.078	0.06	0.983	12.2	2.2		18204

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.06	2.1	94		0.357	0.327	0.214	1.9	1.6

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	2.068	28.386	17663	839	87.976	0.193	0.1894	0.189	0.2582	0.2581	31.793

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]
0.414		0.586	-1.409		0.672

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.363
r_dihedral_angle_3_deg	14.457
r_lrange_it	10.481
r_dihedral_angle_2_deg	7.333
r_dihedral_angle_1_deg	6.671
r_scangle_it	6.439
r_mcangle_it	5.567
r_scbond_it	4.497
r_mcbond_it	3.77
r_angle_refined_deg	1.832
r_nbtor_refined	0.301
r_symmetry_nbd_refined	0.266
r_nbd_refined	0.225
r_xyhbond_nbd_refined	0.217
r_symmetry_xyhbond_nbd_refined	0.177
r_ncsr_local_group_1	0.15
r_chiral_restr	0.12
r_bond_refined_d	0.009
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2417
Nucleic Acid Atoms
Solvent Atoms	148
Heterogen Atoms	108

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data scaling
HKL-2000	data reduction
PHASER	phasing