6JC8 | pdb_00006jc8

Crystal structure of aminotransferase CrmG from Actinoalloteichus sp. WH1-2216-6 in complex with amino donor L-Glu

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5DDS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	293	0.2M Sodium acetate, 0.1M TRIS pH 8.5, 32% PEG 3350, 2% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.09	α = 106.6
b = 83.93	β = 109.11
c = 88.459	γ = 95.13

Symmetry
Space Group	P 1

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 PILATUS3 6M		2016-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.9785	SSRF	BL19U1

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	49.46	95	0.122	0.141	0.071	0.992	8.6	3.9		96761

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)
1	2.25	2.29	95.5		0.628	0.728	0.368	0.772		3.9

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	5DDS	2.25	49.46	92048	4706	95	0.1788	0.1769	0.18	0.2146	0.22	RANDOM	29.293

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]
0.12	0.15	-0.25	-0.31	-0.46	0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.328
r_dihedral_angle_4_deg	20.792
r_dihedral_angle_3_deg	15.447
r_dihedral_angle_1_deg	6.864
r_angle_refined_deg	1.584
r_angle_other_deg	1.31
r_chiral_restr	0.073
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.328
r_dihedral_angle_4_deg	20.792
r_dihedral_angle_3_deg	15.447
r_dihedral_angle_1_deg	6.864
r_angle_refined_deg	1.584
r_angle_other_deg	1.31
r_chiral_restr	0.073
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15832
Nucleic Acid Atoms
Solvent Atoms	548
Heterogen Atoms	112

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	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.