3CVL | pdb_00003cvl

Structure of Peroxisomal Targeting Signal 1 (PTS1) binding domain of Trypanosoma brucei Peroxin 5 (TbPEX5)complexed to T. brucei Phosphofructokinase (PFK) PTS1 peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FCH	PDB code 1FCH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.8	298	2.3M Potassium acetate, 0.1M sodium citrate monohydrate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.89	34.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.39	α = 90
b = 66.36	β = 105.13
c = 49.68	γ = 90

Symmetry
Space Group	P 1 21 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	RIGAKU SATURN 944	Osmic VariMax optics	2006-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF

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	2.08	26.4	97.6	0.096	6.5	3.27	16165	16165			25.52

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)
	2.08	2.15	85.4		0.317	2.1	2.73

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	PDB code 1FCH	2.15	26.17	14844	753	97.36	0.215	0.212	0.22	0.278	0.23	RANDOM	23.242

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]
-0.02		-0.01	-0.03		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.186
r_dihedral_angle_3_deg	15.802
r_dihedral_angle_4_deg	14.135
r_dihedral_angle_1_deg	6.712
r_scangle_it	2.502
r_scbond_it	1.725
r_angle_refined_deg	1.368
r_mcangle_it	1.078
r_angle_other_deg	1.008
r_mcbond_it	0.904
r_symmetry_vdw_other	0.238
r_nbd_refined	0.222
r_nbd_other	0.195
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.168
r_symmetry_hbond_refined	0.155
r_mcbond_other	0.151
r_symmetry_vdw_refined	0.147
r_nbtor_other	0.11
r_chiral_restr	0.08
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2332
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
Crystal	data collection
d*TREK	data reduction
d*TREK	data scaling
MOLREP	phasing