9DHH | pdb_00009dhh

DHODH in complex with Compound 8

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 NaAcetate pH4.8, 2.0 M (NH4)2SO4 30 % Glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.53	65.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.813	α = 90
b = 90.813	β = 90
c = 122.738	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		2019-06-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0000	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (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	1.49	78.65	99.6	0.052	0.999	13.75	3.5		95535

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.49	1.74	99.9		0.493	0.831	3.01	3.5

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	1.49	78.65	91230	4305	99.61	0.12703	0.12568	0.1353	0.15573	0.163	RANDOM	24.291

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]
0.21	0.1		0.21		-0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.062
r_dihedral_angle_4_deg	17.584
r_dihedral_angle_3_deg	11.298
r_dihedral_angle_1_deg	5.961
r_angle_other_deg	2.072
r_angle_refined_deg	1.855
r_chiral_restr	0.117
r_bond_refined_d	0.018
r_gen_planes_refined	0.012
r_gen_planes_other	0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.062
r_dihedral_angle_4_deg	17.584
r_dihedral_angle_3_deg	11.298
r_dihedral_angle_1_deg	5.961
r_angle_other_deg	2.072
r_angle_refined_deg	1.855
r_chiral_restr	0.117
r_bond_refined_d	0.018
r_gen_planes_refined	0.012
r_gen_planes_other	0.012
r_bond_other_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2810
Nucleic Acid Atoms
Solvent Atoms	315
Heterogen Atoms	154

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	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.