6SYP

Human DHODH bound to inhibitor IPP/CNRS-A017

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5MUT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.8	293	32% PEG 400 0.2M KSCN 0.2M NaBr 0.1M acetate 4.8

Crystal Properties
Matthews coefficient	Solvent content
3.38	63.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.565	α = 90
b = 90.565	β = 90
c = 122.387	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	PIXEL	DECTRIS EIGER X 16M		2019-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.999987	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.8	48.293	100	0.999	17.6	9		54364

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.84			0.691

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5MUT	1.8	48.25	54321	2621	99.932	0.183	0.1817	0.2026	29.245

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]
0.418	0.209		0.418		-1.357

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.604
r_dihedral_angle_4_deg	15.815
r_dihedral_angle_3_deg	13.25
r_dihedral_angle_1_deg	6.464
r_lrange_it	4.991
r_lrange_other	4.908
r_scangle_it	3.441
r_scangle_other	3.44
r_mcangle_it	2.344
r_mcangle_other	2.338
r_scbond_it	2.147
r_scbond_other	2.146
r_mcbond_it	1.519
r_mcbond_other	1.518
r_angle_refined_deg	1.365
r_angle_other_deg	1.269
r_nbd_other	0.234
r_symmetry_xyhbond_nbd_refined	0.204
r_nbd_refined	0.195
r_symmetry_nbd_other	0.176
r_nbtor_refined	0.152
r_symmetry_nbd_refined	0.131
r_xyhbond_nbd_refined	0.128
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.062
r_gen_planes_refined	0.007
r_bond_refined_d	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2613
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms	76

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing