5AZ6 | pdb_00005az6

Crystal structure of MBP-Tom20 fusion protein with a 2-residue spacer in the connector helix

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ANF	1ANF, 2V1T
experimental model	PDB	2V1T	1ANF, 2V1T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	293	16% PEG 3350, 0.2M Disodium malonate, 0.1M HEPES (pH7.3)

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.906	α = 90
b = 81.227	β = 106.38
c = 109.89	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	CCD	RAYONIX MX-225		2011-06-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32XU	1.0	SPring-8	BL32XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.56	50	99.9	11	3.79		35889

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	1ANF, 2V1T	2.56	24.72	34036	1784	99.24	0.20625	0.20337	0.21	0.25972	0.26	RANDOM	60.183

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]
-0.06		-0.19	-0.23		0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.03
r_dihedral_angle_4_deg	21.131
r_dihedral_angle_3_deg	20.447
r_long_range_B_refined	9.74
r_long_range_B_other	9.739
r_dihedral_angle_1_deg	7.705
r_scangle_other	6.261
r_mcangle_other	5.973
r_mcangle_it	5.972
r_scbond_it	4.139
r_scbond_other	4.138
r_mcbond_it	3.966
r_mcbond_other	3.963
r_angle_refined_deg	1.718
r_angle_other_deg	1.124
r_chiral_restr	0.096
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6754
Nucleic Acid Atoms
Solvent Atoms	21
Heterogen Atoms	46

Software

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