9DHG | pdb_00009dhg

DHODH in complex with Compound 5

X-RAY DIFFRACTION

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	65.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.815	α = 90
b = 90.815	β = 90
c = 122.859	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		2021-01-28	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)	Rrim I (All)	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	1.386	78.65	100	0.098	0.102	0.029	0.999	14.1	12.4		118898

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.386	1.41	100		2.271	2.367	0.665	0.5634	1.3	12.65

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	1.386	78.65	113169	5727	99.98	0.11853	0.11748	0.1263	0.13911	0.1474	RANDOM	24.54

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]
0.2	0.1		0.2		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.648
r_dihedral_angle_4_deg	19.029
r_dihedral_angle_3_deg	12.385
r_dihedral_angle_1_deg	6.083
r_angle_refined_deg	1.677
r_angle_other_deg	1.561
r_chiral_restr	0.101
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_bond_other_d	0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.648
r_dihedral_angle_4_deg	19.029
r_dihedral_angle_3_deg	12.385
r_dihedral_angle_1_deg	6.083
r_angle_refined_deg	1.677
r_angle_other_deg	1.561
r_chiral_restr	0.101
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_bond_other_d	0.009
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2797
Nucleic Acid Atoms
Solvent Atoms	291
Heterogen Atoms	163

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.