2PBZ

Crystal structure of an IMP biosynthesis protein PurP from Thermococcus kodakaraensis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.6	298	0.2M NaCl, 0.1M Na-acetate, 30% MPD, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 4.60

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.342	α = 90
b = 87.4	β = 90
c = 175.907	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	ADSC QUANTUM 315	MIRRORS	2007-02-16	M	SINGLE WAVELENGTH
2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A		NSLS	X29A
2	SYNCHROTRON	NSLS BEAMLINE X12C		NSLS	X12C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.5	50	94.7	0.05	12.5	12		33174			25.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.59	68.1		0.3	1	5.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	SAD	THROUGHOUT	2.5	31	2	33174	29269	733	84.5	0.276	0.276	0.28	0.3	0.31	RANDOM	55.3

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]
8.68			-4.42		-4.26

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.2
c_angle_deg	1.7
c_improper_angle_d	1.08
c_bond_d	0.01
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7083
Nucleic Acid Atoms
Solvent Atoms	240
Heterogen Atoms	93

Software

Software
Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing
SHELXD	phasing