5T26 | pdb_00005t26

Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase from Escherichia coli.

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.1	293	20% PEG 3350 200 mM Sodium Tartrate 14.7 mM HEPES pH 7.1

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.714	α = 90
b = 161.492	β = 90
c = 137.325	γ = 90

Symmetry
Space Group	C 2 2 21

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 200K	VeriMaxHF	2015-08-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	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	2.1	81	99.9	0.142	0.052	14.4	6.8		35248

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.14			0.462	0.236	0.968

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	1yxc	2.1	27.51	35248	1850	99.77	0.1703	0.1683	0.18	0.2071	0.21	RANDOM	16.603

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]
0.05			-0.22		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.472
r_dihedral_angle_4_deg	21.853
r_dihedral_angle_3_deg	14.852
r_dihedral_angle_1_deg	7.155
r_angle_refined_deg	1.695
r_angle_other_deg	1.442
r_chiral_restr	0.087
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.472
r_dihedral_angle_4_deg	21.853
r_dihedral_angle_3_deg	14.852
r_dihedral_angle_1_deg	7.155
r_angle_refined_deg	1.695
r_angle_other_deg	1.442
r_chiral_restr	0.087
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4421
Nucleic Acid Atoms
Solvent Atoms	514
Heterogen Atoms	2037

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
SCALEPACK	data scaling
PHASER	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.