4KM2 | pdb_00004km2

Crystal structure of Dihydrofolate reductase from Mycobacterium tuberculosis in an open conformation in complex with trimethoprim

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	0.05M KCl, 0.01M MgCl2, 15% PEG 6000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.16	α = 90
b = 65.28	β = 90
c = 79.75	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	CCD	MAR CCD 165 mm		2010-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.00000	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.4	50.515	99	0.104	13.5	8.9	65906	65906	2	2

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	1.4	1.48	98		0.771	0.771	1	8.8	9385

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1.4	20.99	65906	65797	3336	98.79	0.1437	0.1406	0.14	0.2008	0.2	RANDOM	16.479

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]
			0.04		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	35.004
r_dihedral_angle_2_deg	30.445
r_dihedral_angle_4_deg	16.656
r_dihedral_angle_3_deg	13.957
r_sphericity_bonded	13.709
r_rigid_bond_restr	6.899
r_dihedral_angle_1_deg	6.715
r_angle_refined_deg	2.432
r_chiral_restr	0.184
r_bond_refined_d	0.024

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	35.004
r_dihedral_angle_2_deg	30.445
r_dihedral_angle_4_deg	16.656
r_dihedral_angle_3_deg	13.957
r_sphericity_bonded	13.709
r_rigid_bond_restr	6.899
r_dihedral_angle_1_deg	6.715
r_angle_refined_deg	2.432
r_chiral_restr	0.184
r_bond_refined_d	0.024
r_gen_planes_refined	0.016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2488
Nucleic Acid Atoms
Solvent Atoms	609
Heterogen Atoms	104

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
PHASER	phasing

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.