3B8X | pdb_00003b8x

Crystal structure of GDP-4-keto-6-deoxymannose-3-dehydratase (ColD) H188N mutant with bound GDP-perosamine

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	batch	6	298	28% PEG 3400, 400 mM MgCl2, 100 mM MES, 2 mM 2-oxoglutarate, 10 mM GDP-perosamine, pH 6.0, batch, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.411	α = 90
b = 98.123	β = 90
c = 119.94	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	BRUKER	montell optics	2007-07-08		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE

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	1.7	30	92.4	0.085	16.24	5.78	81755	75510	2	2

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	1.7	1.79	86		0.408	0.408	3.16	2.54	9941

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2GMU	1.7	30	83883	75464	7680	92.4	0.177	0.177	0.173	0.17	0.26	random	21.268

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]

RMS Deviations
Key	Refinement Restraint Deviation
t_dihedral_angle_d	17.5
t_angle_deg	1.9
t_bond_d	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6198
Nucleic Acid Atoms
Solvent Atoms	665
Heterogen Atoms	126

Software

Software
Software Name	Purpose
SAINT	data scaling
EPMR	phasing
TNT	refinement
PDB_EXTRACT	data extraction
SAINT	data reduction
SADABS	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.