Experiment: 9N5S

Glutarate L-2-hydroxylase K270C mutant-5'-Mal-C2-GC DNA conjugate

X-RAY DIFFRACTION

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	20 % v/v Glycerol, 5 % w/v PEG 3350, 0.05 M Bis-Tris pH 7, 1 M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.44	64.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.525	α = 90
b = 122.525	β = 90
c = 136.661	γ = 90

Symmetry
Space Group	I 4 2 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	2.73	53.65	100	0.381	0.395	0.105	0.995	7.4	26.7		14176

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)
	2.73	2.86	100		2.667	2.764	0.726	0.865	1.7	27.6

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	2.73	50.911	14147	674	99.767	0.188	0.1865	0.1864	0.2197	0.2197	58.77

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]
3.04			3.04		-6.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.006
r_dihedral_angle_3_deg	15.443
r_dihedral_angle_6_deg	14.506
r_lrange_it	12.189
r_scangle_it	9.918
r_mcangle_it	8.888
r_scbond_it	7.134
r_dihedral_angle_1_deg	6.615
r_mcbond_it	6.032
r_angle_refined_deg	1.861

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.006
r_dihedral_angle_3_deg	15.443
r_dihedral_angle_6_deg	14.506
r_lrange_it	12.189
r_scangle_it	9.918
r_mcangle_it	8.888
r_scbond_it	7.134
r_dihedral_angle_1_deg	6.615
r_mcbond_it	6.032
r_angle_refined_deg	1.861
r_nbtor_refined	0.314
r_symmetry_nbd_refined	0.227
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.167
r_chiral_restr	0.118
r_symmetry_xyhbond_nbd_refined	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2357
Nucleic Acid Atoms
Solvent Atoms	40
Heterogen Atoms	11

Software

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.