3MCV | pdb_00003mcv

Structure of PTR1 from Trypanosoma brucei in ternary complex with 2,4-diamino-5-[2-(2,5-dimethoxyphenyl)ethyl]thieno[2,3-d]-pyrimidine and NADP+

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	291	2.8 M sodium acetate, 50 mM sodium citrate, 1mM DTT, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.502	α = 90
b = 89.819	β = 115.49
c = 82.26	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						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97857	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.7	40.761	98.5	0.061	0.061	19.7	5.7	105672	105672

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.79	97.4		0.308	0.308	2.4	5.5	15226

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.7	38.98	105645	5310	98.35	0.137	0.135	0.1447	0.167	0.1729	RANDOM	13.678

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]
-1.31		-0.61	1.7		-0.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.109
r_dihedral_angle_4_deg	18.323
r_dihedral_angle_3_deg	12.603
r_dihedral_angle_1_deg	5.689
r_scangle_it	4.728
r_scbond_it	3.555
r_mcangle_it	2.471
r_mcbond_it	2.174
r_angle_refined_deg	1.454
r_angle_other_deg	0.935
r_mcbond_other	0.531
r_symmetry_vdw_other	0.263
r_nbd_refined	0.21
r_nbd_other	0.192
r_symmetry_hbond_refined	0.18
r_nbtor_refined	0.174
r_symmetry_vdw_refined	0.172
r_xyhbond_nbd_refined	0.148
r_nbtor_other	0.086
r_chiral_restr	0.075
r_bond_refined_d	0.012
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	7453
Nucleic Acid Atoms
Solvent Atoms	793
Heterogen Atoms	300

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction