1T25 | pdb_00001t25

Plasmodium falciparum lactate dehydrogenase complexed with NADH and 3-hydroxyisoxazole-4-carboxylic acid

X-RAY DIFFRACTION

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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
2.3	40

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.241	α = 90
b = 87.185	β = 90
c = 92.094	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		2002-01-01	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	1.9	29.75	99.8	0.066	19.5	4.1	26093	24119	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	1.9	1.99	100		0.227	4.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1LDG	1.9	29.75	26093	24119	1290	97.21	0.15351	0.15351	0.15179	0.16	0.18576	RANDOM	12.609

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]
-1.11			1.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.151
r_dihedral_angle_1_deg	4.037
r_scangle_it	3.879
r_scbond_it	2.352
r_angle_refined_deg	1.667
r_mcangle_it	1.437
r_angle_other_deg	1.236
r_symmetry_hbond_refined	1.156
r_mcbond_it	0.782
r_nbtor_other	0.631
r_nbd_refined	0.216
r_nbd_other	0.187
r_symmetry_vdw_other	0.185
r_symmetry_vdw_refined	0.137
r_xyhbond_nbd_refined	0.129
r_chiral_restr	0.09
r_xyhbond_nbd_other	0.084
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2383
Nucleic Acid Atoms
Solvent Atoms	233
Heterogen Atoms	59

Software

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