2E25 | pdb_00002e25

The Crystal Structure of the T109S mutant of E. coli Dihydroorotase complexed with an inhibitor 5-fluoroorotate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XGE	PDB ENTRY 1XGE chain A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.25	277	14% PEG 3350, 0.1M MES, 75mM MgCl2, 0.15M KCl, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.61	α = 90
b = 72.61	β = 90
c = 176.12	γ = 90

Symmetry
Space Group	P 41 21 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	CCD	MARMOSAIC 300 mm CCD		2006-04-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.9793	APS	23-ID-B

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	2.2	30	60.9	0.043	19	6.1		16140		2	73.8

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	2.2	2.24	38.2		0.203	2.1	3.4	462

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 (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 1XGE chain A	2.7	30	13623	10367	490	75.8	0.22023	0.21838	0.23	0.25677	0.28	RANDOM	63

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]
-0.29			-0.29		0.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.841
r_dihedral_angle_4_deg	16.401
r_dihedral_angle_3_deg	12.952
r_dihedral_angle_1_deg	5.346
r_mcangle_it	3.055
r_scangle_it	2.919
r_mcbond_it	2.307
r_scbond_it	1.887
r_angle_refined_deg	0.932
r_angle_other_deg	0.695
r_mcbond_other	0.434
r_nbd_refined	0.194
r_symmetry_vdw_other	0.184
r_nbtor_refined	0.166
r_nbd_other	0.156
r_xyhbond_nbd_refined	0.133
r_symmetry_hbond_refined	0.131
r_nbtor_other	0.077
r_metal_ion_refined	0.072
r_symmetry_vdw_refined	0.057
r_chiral_restr	0.052
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2693
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms	14

Software

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