Experiment: 2EKD

Structural study of Project ID PH0250 from Pyrococcus horikoshii OT3

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	5.3	291	40%(v/v) 1,2-propanediol, Acetate pH 4.5, 0.05M Ca(OAc)2, pH 5.3, MICROBATCH, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.471	α = 90
b = 158.026	β = 90
c = 163.347	γ = 90

Symmetry
Space Group	C 2 2 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	IMAGE PLATE	RIGAKU RAXIS V		2006-04-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	0.97907	SPring-8	BL26B1

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	2.3	30	100	0.081	20.8	7.4	54164	54164			30.846

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	2.3	2.38	100		0.148	12.16	7.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	TROUGHOUT	2.3	29.94	53905	53905	2656	100	0.19	0.19	0.188	0.1882	0.225	0.2243	RAMDOM	31.8

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]
-1.31			-0.02		1.32

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.5
c_angle_deg	1.3
c_improper_angle_d	0.8
c_bond_d	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9764
Nucleic Acid Atoms
Solvent Atoms	663
Heterogen Atoms	3

Software

Software
Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling