2PQK | pdb_00002pqk

X-ray crystal structure of human Mcl-1 in complex with Bim BH3

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	0.2M zinc acetate, 0.1M imidazole, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.087	α = 90
b = 71.846	β = 90
c = 118.145	γ = 90

Symmetry
Space Group	I 2 2 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	CCD	ADSC QUANTUM 315		2006-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C		APS	24-ID-C

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	34.6	99	0.062	11.9	6.9		15537

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	2.07	95.5		0.335		5.6	1465

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	SAD	THROUGHOUT	2	34.6	15537	776	98.46	0.196	0.194	0.1931	0.229	0.2342	RANDOM	36.035

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]
-0.62			-0.86		1.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.179
r_dihedral_angle_4_deg	16.967
r_dihedral_angle_3_deg	14.437
r_dihedral_angle_1_deg	4.32
r_scangle_it	3.117
r_scbond_it	1.941
r_mcangle_it	1.211
r_angle_refined_deg	1.091
r_mcbond_it	0.646
r_nbtor_refined	0.298
r_symmetry_vdw_refined	0.282
r_metal_ion_refined	0.279
r_nbd_refined	0.21
r_xyhbond_nbd_refined	0.175
r_symmetry_hbond_refined	0.173
r_symmetry_metal_ion_refined	0.103
r_chiral_restr	0.081
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1352
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms	4

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing