6ERK | pdb_00006erk

Crystal structure of diaminopelargonic acid aminotransferase from Psychrobacter cryohalolentis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QJ5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIQUID DIFFUSION	6.1	293	Sodium Citrate 0.1M pH 6.1; Potassium Sodium Tartrate 0.2M; Ammonium sulfate 1.6M

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 182.069	α = 90
b = 67.91	β = 128.81
c = 118.07	γ = 90

Symmetry
Space Group	C 1 2 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 PILATUS 6M-F		2016-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0	SPring-8	BL41XU

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	1.6	70.94	97	0.106	0.115	0.045	0.997	10.6	6.4		143372

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	1.6	1.63	98.6		0.836	0.908	0.35	0.752		6.5

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	1QJ5	1.6	70.94	136275	7082	96.84	0.1489	0.1469	0.15	0.1883	0.19	RANDOM	17.872

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]
4.72		5.28	-4.94		0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.664
r_sphericity_free	34.911
r_dihedral_angle_4_deg	14.132
r_dihedral_angle_3_deg	13.123
r_sphericity_bonded	12.95
r_dihedral_angle_1_deg	6.418
r_rigid_bond_restr	3.449
r_angle_other_deg	2.131
r_angle_refined_deg	1.974
r_chiral_restr	0.124

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.664
r_sphericity_free	34.911
r_dihedral_angle_4_deg	14.132
r_dihedral_angle_3_deg	13.123
r_sphericity_bonded	12.95
r_dihedral_angle_1_deg	6.418
r_rigid_bond_restr	3.449
r_angle_other_deg	2.131
r_angle_refined_deg	1.974
r_chiral_restr	0.124
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6402
Nucleic Acid Atoms
Solvent Atoms	742
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
BALBES	phasing
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
Aimless	data scaling

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.