3SFK | pdb_00003sfk

Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM267

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3I65	PDB ENTRY 3I65

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.1	293	1.64-1.74 M ammonium sulfate, 10 mM DTT, 0.1 M sodium acetate, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.586	α = 90
b = 86.586	β = 90
c = 138.167	γ = 120

Symmetry
Space Group	P 64

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 315		2010-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID		APS	19-ID

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	2.95	50	99.8	0.1		7.5	13217	13197	2	2

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	2.95	3	100		0.755	0.1	7.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	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 3I65	2.95	50	2	13217	13197	643	99.72	0.227	0.224	0.2152	0.286	0.2728	RANDOM	114.766

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]
0.94	0.47		0.94		-1.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.679
r_dihedral_angle_4_deg	16.001
r_dihedral_angle_3_deg	14.531
r_dihedral_angle_1_deg	5.136
r_angle_refined_deg	1.057
r_scangle_it	0.837
r_mcangle_it	0.513
r_scbond_it	0.486
r_mcbond_it	0.279
r_chiral_restr	0.062
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2921
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms	67

Software

Software
Software Name	Purpose
HKL-3000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling