9GEM | pdb_00009gem

Crystal structure of NUDT14 complexed with novel compound MA12

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8OTV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	0.2 M sodium formate 20% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.919	α = 90
b = 107.191	β = 93.624
c = 78.114	γ = 90

Symmetry
Space Group	P 1 21 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 XE 16M		2023-07-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	2.015	77.958	89.9	0.996	6.7	7.1		19966

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	2.015	2.338			0.693

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	FREE R-VALUE	2.015	77.958	19966	1068	34.753	0.219	0.2149	0.215	0.2866	0.2872	32.373

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]
-0.829		0.193	1.193		-0.385

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_2_deg	26.073
r_dihedral_angle_2_deg	18.699
r_dihedral_angle_3_deg	15.658
r_dihedral_angle_6_deg	14.496
r_lrange_it	12.116
r_lrange_other	12.116
r_dihedral_angle_1_deg	9.15
r_scangle_it	8.115
r_scangle_other	8.114
r_mcangle_it	7.376
r_mcangle_other	7.375
r_scbond_it	5.11
r_scbond_other	5.109
r_mcbond_it	4.681
r_mcbond_other	4.679
r_angle_refined_deg	2.269
r_angle_other_deg	0.882
r_symmetry_nbd_refined	0.232
r_symmetry_xyhbond_nbd_refined	0.228
r_nbd_other	0.218
r_nbd_refined	0.206
r_xyhbond_nbd_refined	0.178
r_symmetry_nbd_other	0.176
r_nbtor_refined	0.175
r_ncsr_local_group_2	0.105
r_ncsr_local_group_3	0.102
r_chiral_restr	0.099
r_ncsr_local_group_1	0.099
r_ncsr_local_group_4	0.099
r_ncsr_local_group_6	0.097
r_ncsr_local_group_5	0.095
r_symmetry_nbtor_other	0.084
r_symmetry_xyhbond_nbd_other	0.048
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6150
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms	84

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
STARANISO	data scaling
PHASER	phasing