1U4S | pdb_00001u4s

Plasmodium falciparum lactate dehydrogenase complexed with 2,6-naphthalenedisulphonic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LDG	PDB model 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
2.4	48.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.094	α = 90
b = 86.096	β = 90
c = 91.327	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	IMAGE PLATE	MACSCIENCE	Mirrors	2001-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR591	1.5418

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	2	30	90.9	0.055	13.6	6	19866	19866	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	2	2.15	79.5		0.174	4.1	2	3421

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB model 1LDG	2	29.36	20360	19321	1039	94.25	0.13843	0.13843	0.13578	0.15	0.18767	0.2	RANDOM	16.842

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]
-1.6			1.73		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.685
r_scangle_it	3.76
r_scbond_it	2.325
r_angle_refined_deg	1.481
r_mcangle_it	1.336
r_angle_other_deg	0.829
r_mcbond_it	0.77
r_nbd_refined	0.316
r_symmetry_vdw_other	0.291
r_nbd_other	0.24
r_symmetry_vdw_refined	0.171
r_xyhbond_nbd_refined	0.143
r_symmetry_hbond_refined	0.127
r_chiral_restr	0.088
r_nbtor_other	0.084
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_gen_planes_other	0.007
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2322
Nucleic Acid Atoms
Solvent Atoms	235
Heterogen Atoms	18

Software

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