2NL9 | pdb_00002nl9

Crystal structure of the Mcl-1:Bim BH3 complex

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.75	298	0.2M zinc acetate, 0.2M imidazole, 2mM TCEP, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.38	α = 90
b = 70.08	β = 90
c = 117.18	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	monochrometer	2005-11-08	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9791, 0.9792, 0.9715	NSLS	X29A

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	1.5	50	85.1	0.067	160.5	10.9		29809

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	1.5	1.55	28.2		0.503			976

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	MAD	THROUGHOUT	1.55	34.12	28898	1469	91.11	0.174	0.173	0.2	0.203	0.23	RANDOM	24.336

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]
-0.53			-0.14		0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.736
r_dihedral_angle_4_deg	15.317
r_dihedral_angle_3_deg	12.505
r_dihedral_angle_1_deg	4.407
r_scangle_it	3.59
r_scbond_it	2.491
r_mcangle_it	1.604
r_angle_refined_deg	1.386
r_mcbond_it	1.061
r_nbtor_refined	0.32
r_symmetry_vdw_refined	0.23
r_symmetry_hbond_refined	0.217
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.157
r_chiral_restr	0.086
r_metal_ion_refined	0.044
r_symmetry_metal_ion_refined	0.043
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1349
Nucleic Acid Atoms
Solvent Atoms	201
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXE	model building