2A92

Crystal structure of lactate dehydrogenase from Plasmodium vivax: complex with NADH

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.1	291	PEG 5000 monoethylether, Ammonium Sulphate, Mes, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.593	α = 90
b = 128.636	β = 90
c = 130.58	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	ADSC QUANTUM 4		2004-11-24	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 Merge 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	91.29	98.2	0.108	11.8	3.9	98204	98204		2	26.95

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.1	97.5	97.3	0.434	2.4	3.8	9639

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	PDB Entry 1T2C	2.04	91.29	90148	85849	4299	97.82	0.197	0.197	0.194	0.236	RANDOM	9.716

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]
1.44			-1.85		0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.529
r_dihedral_angle_3_deg	14.824
r_dihedral_angle_4_deg	14.051
r_dihedral_angle_1_deg	7.112
r_scangle_it	2.752
r_scbond_it	1.9
r_angle_refined_deg	1.525
r_mcangle_it	1.08
r_mcbond_it	0.721
r_nbtor_refined	0.296

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.529
r_dihedral_angle_3_deg	14.824
r_dihedral_angle_4_deg	14.051
r_dihedral_angle_1_deg	7.112
r_scangle_it	2.752
r_scbond_it	1.9
r_angle_refined_deg	1.525
r_mcangle_it	1.08
r_mcbond_it	0.721
r_nbtor_refined	0.296
r_symmetry_vdw_refined	0.209
r_nbd_refined	0.201
r_symmetry_hbond_refined	0.157
r_xyhbond_nbd_refined	0.146
r_chiral_restr	0.108
r_bond_refined_d	0.015
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9596
Nucleic Acid Atoms
Solvent Atoms	480
Heterogen Atoms	176

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
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 R01GM133198.