4TOT

Crystal structure of rat cyclophilin D in complex with a potent nonimmunosuppressive inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		in-house structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291.15	100 mM MES pH 6.5, 5% (v/v) PEG 400, 2M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.197	α = 89.95
b = 57.286	β = 83.81
c = 75.274	γ = 89.86

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	Bruker Platinum 135		2012-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	2.39	45.47	90.94	7.82	3.22		30008			33.71

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	in-house structure	2.39	30.3	29998	1517	90.94	0.1978	0.1961	0.2298	RANDOM	19.55

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]
-0.1115	-0.4018	1.2694	-2.0381	-0.9374	2.1496

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	14.98
t_omega_torsion	2.83
t_angle_deg	1.1
t_bond_d	0.009
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4976
Nucleic Acid Atoms
Solvent Atoms	298
Heterogen Atoms	1376

Software

Software
Software Name	Purpose
BUSTER	refinement