3IHF | pdb_00003ihf

Crystal structure of mouse Bcl-xl mutant (R139A) at pH 5.0

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PQ0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	295	1.45M Ammonium sulphate, Tri-Na citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.353	α = 89.98
b = 56.525	β = 89.93
c = 96.443	γ = 89.82

Symmetry
Space Group	P 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	CCD	ADSC QUANTUM 270	mirrors	2008-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 6C1	1.0000	PAL/PLS	6C1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.02	50	90.42	0.05	0.09	32.5	2.3	39513	29247			32.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.02	2.09	63.7		0.05	0.11	5.6	1.8	3141

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1PQ0	2.28	50	39513	29247	1538	90.42	0.19685	0.19685	0.19311	0.2	0.26623	0.26	RANDOM	32.856

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]
-2.87	0.28	-0.32	4.33	-0.29	-1.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.36
r_dihedral_angle_4_deg	20.675
r_dihedral_angle_3_deg	20.507
r_dihedral_angle_1_deg	8.052
r_scangle_it	5.264
r_scbond_it	3.36
r_mcangle_it	2.36
r_angle_refined_deg	2.308
r_mcbond_it	1.25
r_nbtor_refined	0.316
r_symmetry_vdw_refined	0.316
r_nbd_refined	0.269
r_chiral_restr	0.189
r_xyhbond_nbd_refined	0.189
r_symmetry_hbond_refined	0.188
r_symmetry_metal_ion_refined	0.162
r_metal_ion_refined	0.106
r_bond_refined_d	0.024
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4888
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms

Software

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