8DHH | pdb_00008dhh

DHODH IN COMPLEX WITH LIGAND 29

X-RAY DIFFRACTION

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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	4.8	293	0.10 M Sodium Acetate pH4.8, 2.30 M (NH4)2SO4, 30% Glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.61	65.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.778	α = 90
b = 91.778	β = 90
c = 122.48	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-F		2019-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.00002	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	2.02	79.48	99.5	0.068	0.073	0.999	21.61	8		39538			38.636

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	2.02	2.27	99.4		0.499	0.533	0.954	4.84	8.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	1D3G	2.02	79.48	37675	1863	99.53	0.187	0.1856	0.194	0.2156	0.218	RANDOM	39.505

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]
0.87	0.43		0.87		-2.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.007
r_dihedral_angle_4_deg	16.153
r_dihedral_angle_3_deg	11.734
r_dihedral_angle_1_deg	6.252
r_angle_refined_deg	1.502
r_angle_other_deg	1.226
r_chiral_restr	0.075
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2732
Nucleic Acid Atoms
Solvent Atoms	284
Heterogen Atoms	102

Software

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