3FDL | pdb_00003fdl

Bim BH3 peptide in complex with Bcl-xL

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2P1L	PDB ENTRY 2P1L without Beclin BH3 ligand

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	1M Sodium citrate, 0.1M Sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.82	32.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.111	α = 90
b = 35.684	β = 111.54
c = 62.76	γ = 90

Symmetry
Space Group	C 1 2 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	IMAGE PLATE	RIGAKU RAXIS IV++	AXCO capillary optic	2007-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54

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	1.78	50	96	0.046		5.7	14858	14264

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)
	1.78	1.84	94.9		0.163	11.1	5.8	1463

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2P1L without Beclin BH3 ligand	1.78	29.19	14140	13529	728	95.68	0.16295	0.16295	0.16045	0.20769	0.2216	RANDOM	16.516

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]
-0.55		-0.41	-0.49		0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.935
r_dihedral_angle_4_deg	18.68
r_dihedral_angle_3_deg	14.603
r_scangle_it	4.92
r_dihedral_angle_1_deg	4.752
r_scbond_it	3.339
r_mcangle_it	2.055
r_angle_refined_deg	1.452
r_mcbond_it	1.186
r_chiral_restr	0.265
r_bond_refined_d	0.015
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1385
Nucleic Acid Atoms
Solvent Atoms	209
Heterogen Atoms

Software

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