4ND1 | pdb_00004nd1

Crystal structure of the lactate dehydrogenase from cryptosporidium parvum complexed with cofactor (b-nicotinamide adenine dinucleotide) and inhibitor (oxamic acid)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2EWD	pdb entry 2EWD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	The protein was incubated with 1 mM pyruvate and 100 uM APAD+ for 1 hour on ice prior to crystallization. Reservoir solution was 1.45-1.65 M ammonium sulfate in 0.1 M sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.54	65.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.816	α = 90
b = 94.816	β = 90
c = 185.072	γ = 120

Symmetry
Space Group	P 32 2 1

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		2005-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

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	2.15	47.4		0.061		6.7		50521

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	2.15	2.23			0.35		4.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	pdb entry 2EWD	2.15	47.4	45370	5088	95.05	0.21119	0.20847	0.21	0.23571	0.23	RANDOM	48.457

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]
1.31	1.31		1.31		-4.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.326
r_dihedral_angle_4_deg	15.651
r_dihedral_angle_3_deg	11.462
r_dihedral_angle_1_deg	4.845
r_angle_refined_deg	0.954
r_angle_other_deg	0.662
r_chiral_restr	0.048
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4708
Nucleic Acid Atoms
Solvent Atoms	150
Heterogen Atoms	124

Software

Software
Software Name	Purpose
REFMAC	refinement
CNS	refinement
d*TREK	data scaling
CNS	phasing