2DZ9

Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horikoshii Complexed with biotinyl-5'-AMP, Mutation D104A

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	5.2	295	PEG20K, Acetate, NaOH, ATP, Biotin, pH 5.2, microbatch, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.082	α = 90
b = 82.56	β = 100.44
c = 72.24	γ = 90

Symmetry
Space Group	P 1 21 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	IMAGE PLATE	RIGAKU RAXIS IV	mirrors	2006-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.84	50	98.2	0.075	0.057	14.3	3.1	38110	37434			25.1

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)
	1.84	1.91	93.3		0.442	0.369	3.6	2.9	3364

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 2DXT	1.84	28.48	38110	37434	1849	98.2	0.192	0.192	0.192	0.228	RANDOM	28

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]
-0.26		3.07	-8.84		9.09

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.5
c_angle_deg	1.2
c_improper_angle_d	0.85
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3668
Nucleic Acid Atoms
Solvent Atoms	453
Heterogen Atoms	76

Software

Software
Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	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 R01GM133198.