1T2E

Plasmodium falciparum lactate dehydrogenase S245A, A327P mutant complexed with NADH and oxamate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LDG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	MPD, Hepes, Imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.1	40

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.066	α = 90
b = 85.336	β = 90
c = 89.714	γ = 90

Symmetry
Space Group	I 2 2 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	CCD	ADSC QUANTUM 4		2001-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.1	1.488	SRS	PX14.1

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	1.85	20	98.8	0.059	21.3	4.9	26293	25934	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.93	96.2		0.289	3.7		3153

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1LDG	1.85	20	24726	23475	1251	94.02	0.15761	0.15761	0.1558	0.19076	RANDOM	17.181

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]
-1.06			1.28		-0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.33
r_scangle_it	5.473
r_dihedral_angle_1_deg	4.249
r_scbond_it	3.371
r_angle_refined_deg	2.375
r_mcangle_it	1.938
r_mcbond_it	1.157
r_symmetry_hbond_refined	0.942
r_nbd_refined	0.358
r_symmetry_vdw_refined	0.287

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.33
r_scangle_it	5.473
r_dihedral_angle_1_deg	4.249
r_scbond_it	3.371
r_angle_refined_deg	2.375
r_mcangle_it	1.938
r_mcbond_it	1.157
r_symmetry_hbond_refined	0.942
r_nbd_refined	0.358
r_symmetry_vdw_refined	0.287
r_chiral_restr	0.174
r_xyhbond_nbd_refined	0.159
r_bond_refined_d	0.023
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2404
Nucleic Acid Atoms
Solvent Atoms	242
Heterogen Atoms	56

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	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.