9CZE | pdb_00009cze

High-Resolution Structure of Human DHODH for Molecular Replacement in Fragment Screening Campaign

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5K9C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.8	293.15	0.1 M sodium acetate trihydrate pH 4.8, 1.8 M ammonium sulfate and 30% (v/v) glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.87	68.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.597	α = 90
b = 90.597	β = 90
c = 123.232	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 PILATUS3 6M		2023-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

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	1.6	48.46	99.9	0.971	11.3	9.8		77597		1

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	1.6	1.63	100		0.595	1.3	9.9

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	1.6	48.46	77550	3937	99.915	0.181	0.1802	0.1802	0.1968	0.1968	23.286

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]
0.006	0.003		0.006		-0.019

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.656
r_dihedral_angle_3_deg	12.253
r_dihedral_angle_2_deg	9.306
r_dihedral_angle_1_deg	5.811
r_lrange_it	5.687
r_scangle_it	2.715
r_mcangle_it	1.737
r_scbond_it	1.662
r_mcbond_it	1.07
r_angle_refined_deg	1.067

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.656
r_dihedral_angle_3_deg	12.253
r_dihedral_angle_2_deg	9.306
r_dihedral_angle_1_deg	5.811
r_lrange_it	5.687
r_scangle_it	2.715
r_mcangle_it	1.737
r_scbond_it	1.662
r_mcbond_it	1.07
r_angle_refined_deg	1.067
r_nbtor_refined	0.304
r_nbd_refined	0.207
r_symmetry_nbd_refined	0.185
r_xyhbond_nbd_refined	0.161
r_chiral_restr	0.077
r_symmetry_xyhbond_nbd_refined	0.075
r_gen_planes_refined	0.005
r_bond_refined_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2602
Nucleic Acid Atoms
Solvent Atoms	281
Heterogen Atoms	80

Software

Software
Software Name	Purpose
REFMAC	refinement
PHASER	phasing
XDS	data reduction

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.