4TT3 | pdb_00004tt3

The Pathway of Binding of the Intrinsically Disordered Mitochondrial Inhibitor Protein to F1-ATPase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V7Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	8.2	295	PEG 4000, Tris-HCl, magnesium chloride, EDTA, ATP, NaCl, spermidine

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.385	α = 90
b = 154.545	β = 90
c = 272.04	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	100	CCD	RAYONIX MX-225		2012-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8726	ESRF	ID23-2

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	3.21	67.12	97.5	0.078	7.6	2.5		73010

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.21	3.28	99.1		2.3	2.5

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	2v7q	3.21	136.02	72985	3688	96.71	0.2443	0.2422	0.24	0.2834	0.28	RANDOM	93.079

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]
-2.32			3.38		-1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.045
r_dihedral_angle_3_deg	10.612
r_dihedral_angle_4_deg	9.464
r_dihedral_angle_1_deg	3.665
r_mcangle_it	1.691
r_mcbond_it	0.946
r_mcbond_other	0.945
r_angle_refined_deg	0.732
r_angle_other_deg	0.655
r_chiral_restr	0.064

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.045
r_dihedral_angle_3_deg	10.612
r_dihedral_angle_4_deg	9.464
r_dihedral_angle_1_deg	3.665
r_mcangle_it	1.691
r_mcbond_it	0.946
r_mcbond_other	0.945
r_angle_refined_deg	0.732
r_angle_other_deg	0.655
r_chiral_restr	0.064
r_bond_refined_d	0.004
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	23918
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms	181

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building
PDB_EXTRACT	data extraction
MOSFLM	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.