7YHE | pdb_00007yhe

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

X-RAY DIFFRACTION

Starting Model(s)

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

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
2.63	53.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.115	α = 90
b = 127.191	β = 90
c = 138.759	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	RAYONIX MX300-HS		2021-06-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 05A	1	NSRRC	TPS 05A

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	1.67	30	99.9	0.055	24.05	4.5		95108

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.67	1.73	100		0.76	0.757	2.02	4.4

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	1.67	27.67	85445	4533	94.35	0.1788	0.178	0.19	0.1936	0.2	RANDOM	16.668

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]
-0.16			-0.15		0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.106
r_dihedral_angle_4_deg	16.537
r_dihedral_angle_3_deg	12.434
r_dihedral_angle_1_deg	6.928
r_angle_other_deg	1.324
r_angle_refined_deg	1.279
r_chiral_restr	0.06
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.106
r_dihedral_angle_4_deg	16.537
r_dihedral_angle_3_deg	12.434
r_dihedral_angle_1_deg	6.928
r_angle_other_deg	1.324
r_angle_refined_deg	1.279
r_chiral_restr	0.06
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5228
Nucleic Acid Atoms
Solvent Atoms	512
Heterogen Atoms	31

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.