9N2U | pdb_00009n2u

Glutarate L-2-hydroxylase N187C mutant-5'-Mal-C6-GC DNA conjugate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2R6S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	0.05 M Bis-Tris pH 7, 1.5 M Lithium sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.27	62.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.083	α = 90
b = 124.083	β = 90
c = 126.932	γ = 90

Symmetry
Space Group	P 4 21 2

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 9M		2023-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.87313	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2.06	126.93	100	0.361	0.373	0.096	0.997	8	28.5		61788

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.06	2.11	100		2.992	3.095	0.789	0.601	1.6	29.7

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	2.06	126.93	61716	3182	99.934	0.201	0.2003	0.2034	0.2228	0.2252	35.675

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]
-0.36			-0.36		0.721

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.972
r_dihedral_angle_6_deg	14.508
r_dihedral_angle_3_deg	13.475
r_lrange_it	8.091
r_lrange_other	8.089
r_scangle_it	6.52
r_scangle_other	6.519
r_dihedral_angle_1_deg	6.246
r_scbond_it	4.315
r_scbond_other	4.298
r_mcangle_other	4.211
r_mcangle_it	4.21
r_mcbond_it	2.964
r_mcbond_other	2.964
r_angle_refined_deg	1.573
r_angle_other_deg	0.513
r_dihedral_angle_other_2_deg	0.51
r_nbd_other	0.221
r_nbd_refined	0.215
r_symmetry_nbd_other	0.209
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.151
r_xyhbond_nbd_refined	0.132
r_symmetry_nbd_refined	0.114
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.075
r_ncsr_local_group_1	0.06
r_gen_planes_other	0.01
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4601
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building