9BKM | pdb_00009bkm

DHODH in complex with Ligand 10

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 NaAcetat_pH4.8, 2.30 M (NH4)2SO4, 30 % Glycerol, 18% (w/v) PEG 4000, 0.1M Na3Citrate pH=5.75

Crystal Properties
Matthews coefficient	Solvent content
3.65	66.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.018	α = 90
b = 91.018	β = 90
c = 121.995	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 PILATUS 6M		2019-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.99989	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.08	78.82	95.1	0.089	0.099	0.998	13.63	5.2		33919

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.08	2.33	88.4		0.498	0.554	0.937	3.84	5.2

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	2.08	78.82	32355	1564	95.04	0.19238	0.19063	0.2	0.22795	0.23	RANDOM	34.763

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]
-0.07	-0.04		-0.07		0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.357
r_dihedral_angle_4_deg	19.288
r_dihedral_angle_3_deg	12.684
r_dihedral_angle_1_deg	6.397
r_angle_refined_deg	1.739
r_angle_other_deg	1.335
r_chiral_restr	0.099
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.357
r_dihedral_angle_4_deg	19.288
r_dihedral_angle_3_deg	12.684
r_dihedral_angle_1_deg	6.397
r_angle_refined_deg	1.739
r_angle_other_deg	1.335
r_chiral_restr	0.099
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2703
Nucleic Acid Atoms
Solvent Atoms	262
Heterogen Atoms	102

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
PHASER	phasing

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.