3BMC | pdb_00003bmc

Structure of Pteridine Reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and substrate (folate)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	2-3M sodium acetate, 10-100mM sodium citrate, pH 4.5, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.441	α = 90
b = 88.596	β = 115.34
c = 81.587	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 RAXIS IV	mirrors			SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54

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	2.6	73.737	81.1	0.068	0.068	9.1	2.2		23556

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	2.6	2.74	74		0.377	0.377	2	2.3	3152

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	2.6	37.67	23539	1224	79.49	0.192	0.189	0.1895	0.244	0.2375	RANDOM	30.712

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]
-4.56		-2.83	7.48		-5.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.998
r_dihedral_angle_4_deg	18.618
r_dihedral_angle_3_deg	17.034
r_dihedral_angle_1_deg	5.444
r_angle_refined_deg	1.46
r_scangle_it	1.239
r_scbond_it	0.92
r_mcangle_it	0.548
r_symmetry_hbond_refined	0.418
r_symmetry_vdw_refined	0.366

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.998
r_dihedral_angle_4_deg	18.618
r_dihedral_angle_3_deg	17.034
r_dihedral_angle_1_deg	5.444
r_angle_refined_deg	1.46
r_scangle_it	1.239
r_scbond_it	0.92
r_mcangle_it	0.548
r_symmetry_hbond_refined	0.418
r_symmetry_vdw_refined	0.366
r_mcbond_it	0.331
r_nbtor_refined	0.303
r_xyhbond_nbd_refined	0.286
r_nbd_refined	0.207
r_chiral_restr	0.097
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7405
Nucleic Acid Atoms
Solvent Atoms	253
Heterogen Atoms	320

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.