7YW9 | pdb_00007yw9

Crystal structure of the triple mutant CmnC-L136Q,S138G,D249Y in complex with alpha-KG

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	20 mM ammonium acetate, 24% v/v polyethylene glycol 400, 0.1 M sodium citrate tribasic dihydrate

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.951	α = 90
b = 126.671	β = 90
c = 140.188	γ = 90

Symmetry
Space Group	I 2 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	80	CCD	ADSC QUANTUM 315r		2022-08-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	0.9732	NSRRC	BL13B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.75	30	99.9	0.052	25.9	4.5		81412

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.81	99.8		0.439	3.07	4.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	2WBO	1.76	25.91	73873	3871	94.8	0.1778	0.1769	0.19	0.1951	0.2	RANDOM	22.33

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]
-0.09			-0.29		0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.486
r_dihedral_angle_4_deg	16.365
r_dihedral_angle_3_deg	13.225
r_dihedral_angle_1_deg	6.978
r_angle_other_deg	1.326
r_angle_refined_deg	1.322
r_chiral_restr	0.066
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.486
r_dihedral_angle_4_deg	16.365
r_dihedral_angle_3_deg	13.225
r_dihedral_angle_1_deg	6.978
r_angle_other_deg	1.326
r_angle_refined_deg	1.322
r_chiral_restr	0.066
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5301
Nucleic Acid Atoms
Solvent Atoms	430
Heterogen Atoms	40

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

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.