3GD3

Crystal structure of a naturally folded murine apoptosis inducing factor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GV4	PDB entry 1GV4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	microbatch under oil	7	298	15% PEG 4000, 0.35M KNO3, pH 7.0, microbatch under oil, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.05	α = 90
b = 80.29	β = 90
c = 419.64	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	103	IMAGE PLATE	MAR scanner 345 mm plate	mirrors	2008-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	1.1	SSRL	BL9-2

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	2.8	408.25	81.12	0.174	0.174		4.97	61080	49548	2	2

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)
	2.8	2.873	69.45		0.715	0.715	1.7	5.06

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1GV4	2.95	46.64	71343	43694	2103	83.42	0.25095	0.24861	0.29965	RANDOM	95.017

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]
-6.06			-0.65		6.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.123
r_dihedral_angle_3_deg	20.869
r_dihedral_angle_4_deg	20.288
r_dihedral_angle_1_deg	6.98
r_scangle_it	3.162
r_scbond_it	1.932
r_angle_refined_deg	1.77
r_mcangle_it	1.559
r_mcbond_it	0.991
r_nbtor_refined	0.308
r_nbd_refined	0.223
r_symmetry_vdw_refined	0.173
r_xyhbond_nbd_refined	0.16
r_symmetry_hbond_refined	0.127
r_chiral_restr	0.103
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14482
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms	212

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling