3PL2 | pdb_00003pl2

Crystal structure of a 5-keto-2-deoxygluconokinase (NCgl0155, Cgl0158) from Corynebacterium glutamicum ATCC 13032 KITASATO at 1.89 A resolution

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	293	0.200M NH4OAc, 30.00% PEG-4000, 0.1M Citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.908	α = 101.86
b = 79.494	β = 95.72
c = 81.703	γ = 92.11

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	CCD	MARMOSAIC 300 mm CCD		2008-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B		APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.89	37.804	97.1	0.065	7.8	2.3	87262	87262			25.396

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.89	1.94	95.8		0.438	0.438	1.2	2	6386

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	2QCV	1.89	37.804	87222	4384	96.98	0.1828	0.1805	0.19	0.2252	0.23	RANDOM	37.5491

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]
0.23	0.42	0.14	-0.49	0.53	0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.535
r_dihedral_angle_4_deg	14.737
r_dihedral_angle_3_deg	14.591
r_dihedral_angle_1_deg	6.691
r_scangle_it	3.121
r_scbond_it	1.938
r_angle_refined_deg	1.574
r_angle_other_deg	1.327
r_mcangle_it	1.211
r_mcbond_it	0.681

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.535
r_dihedral_angle_4_deg	14.737
r_dihedral_angle_3_deg	14.591
r_dihedral_angle_1_deg	6.691
r_scangle_it	3.121
r_scbond_it	1.938
r_angle_refined_deg	1.574
r_angle_other_deg	1.327
r_mcangle_it	1.211
r_mcbond_it	0.681
r_mcbond_other	0.182
r_chiral_restr	0.091
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9480
Nucleic Acid Atoms
Solvent Atoms	577
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	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.