1XO7 | pdb_00001xo7

Crystal structure of cyclophilin from Trypanosoma cruzi

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DYW	1DYW.pdb

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	298	Ammonium Phosphate monobasic, Sodium Acetate, PEG8000, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 25K, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.314	α = 109.55
b = 62.142	β = 104.21
c = 64.638	γ = 104.92

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 4	custom	2004-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	1.0000	ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.61	56.8	93.4	0.103	7.2	1.8	80854	80854	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.61	1.7	89.4		0.55	2	1.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	1DYW.pdb	1.61	56.8	2	80854	80854	4251	93.4	0.179	0.18	0.17899	0.1898	0.19774	0.2096	RANDOM	15.335

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]
-0.53	0.29	0.36	1.11	0.14	-0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.597
r_scangle_it	6.58
r_scbond_it	4.471
r_angle_other_deg	3.668
r_angle_refined_deg	2.61
r_mcangle_it	2.591
r_mcbond_it	1.637
r_symmetry_vdw_other	0.302
r_nbd_other	0.297
r_nbd_refined	0.21
r_chiral_restr	0.189
r_symmetry_vdw_refined	0.177
r_nbtor_other	0.123
r_symmetry_hbond_refined	0.109
r_xyhbond_nbd_refined	0.094
r_bond_refined_d	0.038
r_gen_planes_other	0.022
r_gen_planes_refined	0.014
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5088
Nucleic Acid Atoms
Solvent Atoms	808
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
ELVES	data reduction
ELVES	data scaling
EPMR	phasing