3AJV | pdb_00003ajv

Splicing endonuclease from Aeropyrum pernix

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	295	20mM Tris-HCl (pH 8.0), 750mM KCl, 10% (v/v) glycerol, 0.2M NaCl, 0.1M phosphate-citrate (pH 4.2), 10% (w/v) PEG3000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.334	α = 90
b = 95.334	β = 90
c = 253.819	γ = 120

Symmetry
Space Group	H 3

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 270		2008-12-13	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 270		2008-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	1	Photon Factory	BL-17A
2	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	1.0717	Photon Factory	BL-17A

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	1.7	50	98.5	0.072	14	4.8	92608	90770

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	1.7	1.73	85.1		0.346	3.1

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	SIRAS	THROUGHOUT	1.7	30	92608	88149	4695	98.29	0.21809	0.21809	0.21751	0.2388	0.22893	0.2345	RANDOM	23.45

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]
4.14			4.14		-8.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.09
r_dihedral_angle_4_deg	20.071
r_dihedral_angle_3_deg	15.07
r_dihedral_angle_1_deg	6.227
r_scangle_it	3.965
r_scbond_it	2.475
r_mcangle_it	1.589
r_angle_refined_deg	1.505
r_mcbond_it	0.944
r_chiral_restr	0.105
r_bond_refined_d	0.014
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5336
Nucleic Acid Atoms
Solvent Atoms	549
Heterogen Atoms	62

Software

Software
Software Name	Purpose
HKL-2000	data collection
SHELXCD	phasing
SHELXE	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling