4IGH | pdb_00004igh

High resolution crystal structure of human dihydroorotate dehydrogenase bound with 4-quinoline carboxylic acid analog

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4	296	1.72 M ammonium sulfate, 0.1 M sodium acetate, pH 5.4, 1.5 M sodium chloride, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
3.6	65.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.786	α = 90
b = 90.786	β = 90
c = 122.485	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	CCD	ADSC QUANTUM 315		2012-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97918	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.22	78.62	99.66	0.066	27	7.1	172407	171829	2	2	11.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.22	1.24	100		0.937	2	7	8552

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	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	PDB ENTRY 1D3G	1.3	78.62	2	2	172407	171829	4304	99.53	0.13791	0.13761	0.21	0.14764	0.22	RANDOM

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]
0.23	0.12		0.23		-0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	77.794
r_dihedral_angle_2_deg	36.482
r_sphericity_bonded	18.107
r_dihedral_angle_4_deg	17.627
r_dihedral_angle_3_deg	13.008
r_rigid_bond_restr	10.162
r_dihedral_angle_1_deg	6.462
r_angle_refined_deg	2.583
r_angle_other_deg	1.394
r_chiral_restr	0.233

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	77.794
r_dihedral_angle_2_deg	36.482
r_sphericity_bonded	18.107
r_dihedral_angle_4_deg	17.627
r_dihedral_angle_3_deg	13.008
r_rigid_bond_restr	10.162
r_dihedral_angle_1_deg	6.462
r_angle_refined_deg	2.583
r_angle_other_deg	1.394
r_chiral_restr	0.233
r_bond_refined_d	0.027
r_gen_planes_refined	0.016
r_bond_other_d	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2719
Nucleic Acid Atoms
Solvent Atoms	297
Heterogen Atoms	105

Software

Software
Software Name	Purpose
HKL-3000	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.