8RHT

Crystal Structure of Trypanosoma brucei DHFR in complex with the cofactor and inhibitor P25

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3RG9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	6.5	293	35% w/v PEG4000, 50 mM ammonium sulfate, 50 mM bis-tris, pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
1.6	23.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.92	α = 90
b = 60.928	β = 90
c = 68.882	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2023-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.99989	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.9	60.93	100	0.124	0.147	0.077	0.996	8.6	6.3		4243		2	25.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3.08	100		0.964	1.134	0.592	0.92	2.1	6.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.9	45.64	4027	186	99.98	0.19274	0.18778	0.29797	RANDOM	75.303

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]
0.08			0.01		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.554
r_long_range_B_refined	15.694
r_mcangle_it	9.543
r_dihedral_angle_1_deg	7.097
r_scbond_it	6.065
r_dihedral_angle_2_deg	6.003
r_mcbond_it	5.787
r_angle_refined_deg	1.581
r_chiral_restr	0.119
r_gen_planes_refined	0.007
r_bond_refined_d	0.004
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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_it
r_scangle_other
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	1612
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing