9N56 | pdb_00009n56

Glutarate L-2-hydroxylase K270C mutant-5'-Mal-C2-AGCT 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		295	0.3 M Lithium sulfate, 0.05 M Bis-Tris pH 7, 18 % w/v PEG 1000

Crystal Properties
Matthews coefficient	Solvent content
3.33	63.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.414	α = 90
b = 124.414	β = 90
c = 128.175	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 XE 16M		2023-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976284	Diamond	I03

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	2.25	64.09	100	0.157	0.163	0.043	0.999	15	26.6		48353

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)
	2.25	2.32	100		1.747	1.815	0.493	0.893	2.2	26.5

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.25	51.091	48054	2347	99.431	0.215	0.2136	0.2138	0.2332	0.2359	RANDOM	48.662

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]
-1.071			-1.071		2.141

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.312
r_dihedral_angle_3_deg	12.119
r_dihedral_angle_2_deg	11.636
r_dihedral_angle_1_deg	6.566
r_lrange_it	5.73
r_scangle_it	3.763
r_mcangle_it	3.118
r_scbond_it	2.232
r_mcbond_it	1.924
r_angle_refined_deg	1.244
r_nbtor_refined	0.304
r_nbd_refined	0.192
r_symmetry_nbd_refined	0.177
r_symmetry_xyhbond_nbd_refined	0.161
r_xyhbond_nbd_refined	0.147
r_ncsr_local_group_1	0.061
r_chiral_restr	0.058
r_bond_refined_d	0.005
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4660
Nucleic Acid Atoms
Solvent Atoms	230
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing