Experiment: 1TUF

Crystal structure of Diaminopimelate Decarboxylase from m. jannaschi

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Model built with electron density map calculated using a Platinum derivative.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	291	12% PEG6000, 0.1M Tris-HCl, 20mM MgCl2, 25mM azelaic acid, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.806	α = 90
b = 80.806	β = 90
c = 508.503	γ = 120

Symmetry
Space Group	P 61 2 2

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	BRANDEIS - B4		2001-08-20	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 4		2001-04-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.4	NSLS	X25
2	SYNCHROTRON	CHESS BEAMLINE F2	1.07	CHESS	F2

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
1,2	2.4	30	90.3	0.077	4.9	7.8	36391	36391			45

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.4	2.46	53.4		0.292	4.8		1404

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	SIRAS	THROUGHOUT	Model built with electron density map calculated using a Platinum derivative.	2.4	25	35468	1765	88.3	0.204	0.204	0.2032	0.253	0.2533	RANDOM	40.2

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]
6.6	4.9		6.6		-13.21

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.4
c_scangle_it	3.15
c_mcangle_it	2.16
c_scbond_it	2.09
c_mcbond_it	1.32
c_angle_deg	1.2
c_improper_angle_d	0.71
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6824
Nucleic Acid Atoms
Solvent Atoms	292
Heterogen Atoms	26

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing