4CQ8 | pdb_00004cq8

Plasmodium falciparum dihydroorotate dehydrogenase (DHODH) in complex with Genz-669178

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	CO-CRYSTALS WERE GROWN BY VAPOUR DIFFUSION AT 20 DEGREES C FROM A SOLUTION OF PROTEIN AT 10 MG/ML IN BUFFER (10 MM HEPES PH 7.8, 100 MM SODIUM CHLORIDE, 5% GLYCEROL, 10 MM DTT, 1 MM LDAO) CONTAINING 2 MM L-DIHYDROOROTATE, 2 MM GENZ-669178, 10 MM LDAO, MIXED WITH AN EQUAL VOLUME OF PRECIPITANT (24% PEG 3350, 0.2M LITHIUM CHLORIDE)

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 147.82	α = 90
b = 69.13	β = 103.84
c = 103.85	γ = 90

Symmetry
Space Group	C 1 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	PIXEL	DECTRIS PILATUS 6M		2012-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

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	1.98	50	97.4	0.05	15	3.2		69060			37.56

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	1.98	2.05	85.3		0.49	1.7	2.3

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	OTHER	THROUGHOUT	NONE	1.98	46.86	69057	2784	97.28	0.1708	0.17	0.1769	0.1901	0.2022	RANDOM	52.57

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]
0.4182		2.987	8.0936		-8.5118

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	17.16
t_omega_torsion	2.98
t_angle_deg	1.01
t_bond_d	0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5990
Nucleic Acid Atoms
Solvent Atoms	568
Heterogen Atoms	130

Software

Software
Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling