2C7V | pdb_00002c7v

Structure of Trypanosoma brucei pteridine reductase (PTR1) in ternary complex with cofactor and the antifolate methotrexate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E92	PBD ENTRY 1E92

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7		PROTEIN BUFFER WAS 20 MM TRIS HCL, PH 7.0 WITH 1MM NADP, 1 MM METHOTREXATE AND 20 MM DITHIOTHREITOL, PROTEIN CONCENTRATION WAS 6 MG/ML. HANGING DROP RESERVOIR SOLUTION WAS 0.1 M SODIUM CACODYLATE PH 6.5 AND 1.4 M SODIUM ACETATE.

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.655	α = 90
b = 90.244	β = 115.76
c = 82.841	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	IMAGE PLATE	RIGAKU IMAGE PLATE	MIRRORS	2004-07-30	M	SINGLE WAVELENGTH

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

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	2.2	74.5	99.2	0.06	12.4	2.8		50048

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.26	93.1		0.17	3.5	2.1

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	PBD ENTRY 1E92	2.2	74.54	47369	2534	99.2	0.157	0.153	0.15	0.223	0.22	RANDOM	24.22

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]
-1.87		-0.58	2.67		-1.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.424
r_dihedral_angle_4_deg	20.819
r_dihedral_angle_3_deg	16.943
r_dihedral_angle_1_deg	5.763
r_scangle_it	2.349
r_scbond_it	1.466
r_angle_refined_deg	1.402
r_mcangle_it	1.026
r_mcbond_it	0.584
r_chiral_restr	0.538
r_nbtor_refined	0.297
r_symmetry_vdw_refined	0.229
r_nbd_refined	0.201
r_symmetry_hbond_refined	0.159
r_xyhbond_nbd_refined	0.154
r_bond_refined_d	0.013
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7648
Nucleic Acid Atoms
Solvent Atoms	799
Heterogen Atoms	334

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing