9DHI | pdb_00009dhi

DHODH in complex with Compound 7

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	0.10 M NaAc pH4.8, 2.0 M (NH4)2SO4, 30 % (v/v) Glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.55	65.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.758	α = 90
b = 90.758	β = 90
c = 122.778	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 EIGER2 S 16M		2021-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9999	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.38	78.6	100	0.076	0.022	0.9993	16.523	12.47		120423

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.38	1.403	100		0.561	0.5593	1.301	12.67

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MOLECULAR REPLACEMENT	THROUGHOUT	1.38	78.6	114648	5772	99.99	0.11776	0.11669	0.1261	0.13865	0.1456	RANDOM	23.981

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]
0.1	0.05		0.1		-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.792
r_dihedral_angle_4_deg	20.521
r_dihedral_angle_3_deg	12.104
r_dihedral_angle_1_deg	6.274
r_angle_other_deg	1.467
r_angle_refined_deg	1.444
r_chiral_restr	0.084
r_bond_other_d	0.009
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2797
Nucleic Acid Atoms
Solvent Atoms	323
Heterogen Atoms	163

Software

Software
Software Name	Purpose
autoPROC	data reduction
XDS	data reduction
autoPROC	data scaling
Aimless	data scaling
REFMAC	refinement