8VTC | pdb_00008vtc

Crystal structure of Mycobacterium avium dihydrofolate reductase in complex with NADPH and trimethoprim

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2W3V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277.15	55% MPD, 0.1 M Hepes pH 7.5 and 2 mM DTT

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.251	α = 90
b = 70.251	β = 90
c = 73.511	γ = 90

Symmetry
Space Group	P 41 21 2

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 EIGER X 9M		2019-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.97933	NSLS-II	17-ID-1

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	29.564	99.4	0.024	0.034	0.024	0.999	14	1.8		12872

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	2.05	96.9		0.206	0.292	0.206	0.921	2.9	1.9

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2	29.564	12848	665	99.052	0.171	0.1666	0.1666	0.2403	0.2405	41.22

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]
1.722			1.722		-3.444

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.641
r_lrange_other	15.187
r_lrange_it	15.178
r_dihedral_angle_6_deg	13.582
r_dihedral_angle_3_deg	12.419
r_scangle_it	9.924
r_scangle_other	9.919
r_mcangle_it	8.409
r_mcangle_other	8.406
r_scbond_other	6.95
r_scbond_it	6.949
r_dihedral_angle_1_deg	6.699
r_mcbond_other	5.701
r_mcbond_it	5.697
r_rigid_bond_restr	4.45
r_angle_refined_deg	1.71
r_dihedral_angle_other_2_deg	0.64
r_angle_other_deg	0.555
r_symmetry_nbd_refined	0.406
r_nbd_other	0.311
r_nbd_refined	0.206
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.174
r_xyhbond_nbd_refined	0.144
r_symmetry_xyhbond_nbd_other	0.087
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.066
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1273
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms	70

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
autoPROC	data reduction
XDS	data reduction
Aimless	data scaling
PHASER	phasing