3U2O

Dihydroorotate Dehydrogenase (DHODH) crystal structure in complex with small molecule inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1D3G	pdb entry 1D3G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.8	293	ammonium sulfate, pH 4.8, vapor diffusion, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.41	63.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.028	α = 90
b = 91.028	β = 90
c = 122.465	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	CCD	MARMOSAIC 225 mm CCD		2006-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.90005	SLS	X06SA

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	2.18	48.34	99.8	0.142				31139			26.3

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	2.18	2.27	99.5		0.516

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1D3G	2.18	48.34	31139	1557	99.86	0.1611	0.1588	0.2049	RANDOM	28.9191

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]
0.7	0.35		0.7		-1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.465
r_dihedral_angle_4_deg	18.769
r_dihedral_angle_3_deg	15.04
r_scangle_it	7.447
r_dihedral_angle_1_deg	5.914
r_scbond_it	5.651
r_mcangle_it	3.42
r_mcbond_it	3.104
r_angle_refined_deg	1.437
r_angle_other_deg	0.921
r_mcbond_other	0.745
r_symmetry_vdw_other	0.302
r_nbd_refined	0.209
r_nbd_other	0.206
r_xyhbond_nbd_refined	0.202
r_nbtor_refined	0.176
r_symmetry_hbond_refined	0.166
r_symmetry_vdw_refined	0.14
r_nbtor_other	0.088
r_chiral_restr	0.079
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2793
Nucleic Acid Atoms
Solvent Atoms	256
Heterogen Atoms	91

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling