9IDY | pdb_00009idy

Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00219

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6XXI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.025-0.125 mM carboxylic acid mix, 30-60% precipitant mix (MPD, PEG 1000, PEG 3350), 100 mM Tris-Bicine pH = 8.5

Crystal Properties
Matthews coefficient	Solvent content
3.11	60.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.966	α = 90
b = 104.966	β = 90
c = 160.421	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 EIGER2 X 16M		2021-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.9763	MAX IV	BioMAX

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	1.37	46.09	99.6	0.062	0.065	0.999	14.21	10.56		213272

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	1.37	1.47			2.357	2.943	0.379	0.41

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	1.37	46.09	202613	10597	99.5	0.19152	0.19073	0.2005	0.20585	0.2147	RANDOM	29.199

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]
					0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.122
r_long_range_B_refined	7.285
r_long_range_B_other	7.284
r_scangle_other	6.192
r_dihedral_angle_2_deg	5.972
r_dihedral_angle_1_deg	5.947
r_scbond_it	4.275
r_scbond_other	4.274
r_mcangle_it	3.71
r_mcangle_other	3.71
r_mcbond_it	2.707
r_mcbond_other	2.697
r_angle_refined_deg	1.919
r_angle_other_deg	1.024
r_chiral_restr	0.096
r_bond_refined_d	0.018
r_gen_planes_other	0.016
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5381
Nucleic Acid Atoms
Solvent Atoms	482
Heterogen Atoms	108

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data scaling
DIMPLE	phasing
XDS	data reduction