1DAK | pdb_00001dak

DETHIOBIOTIN SYNTHETASE FROM ESCHERICHIA COLI, COMPLEX REACTION INTERMEDIATE ADP AND MIXED ANHYDRIDE

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DAH	PDB ENTRY 1DAH, WITH NON-PROTEIN ATOMS EXCLUDED

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.68	α = 90
b = 48.19	β = 106.58
c = 61.07	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	CCD	PRINCETON 2K		1997-10-28	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID09		ESRF	ID09

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	1.6	25	99	0.078	16	3.2		86120

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)
1	1.6	1.66	92.4		0.43	2.8	2.6

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-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	DIFFERENCE FOURIER	THROUGHOUT	PDB ENTRY 1DAH, WITH NON-PROTEIN ATOMS EXCLUDED	1.6	20	29418	1505	99	0.184	0.21	RANDOM	13.6

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
p_staggered_tor	15.9
p_planar_tor	3.1
p_scangle_it	1.949
p_mcangle_it	1.335
p_scbond_it	1.227
p_mcbond_it	0.862
p_multtor_nbd	0.258
p_singtor_nbd	0.172
p_chiral_restr	0.081
p_planar_d	0.021
p_angle_d	0.02
p_plane_restr	0.0165
p_bond_d	0.006
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_xyhbond_nbd
p_orthonormal_tor
p_transverse_tor
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1692
Nucleic Acid Atoms
Solvent Atoms	216
Heterogen Atoms	54

Software

Software
Software Name	Purpose
CCP4	model building
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CCP4	phasing