9W2K | pdb_00009w2k

Structural basis of substrate promiscuity in the archaeal RNA-splicing endonuclease from Candidatus Micrarchaeum acidiphilum (ARMAN-2)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4FZ2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	2.0M Ammonium sulfate, 0.1M Sodium acetate tri-hydrate

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.514	α = 114.462
b = 65.648	β = 111.89
c = 71.802	γ = 90.01

Symmetry
Space Group	P 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	ADSC QUANTUM 315r		2013-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0	SPring-8	BL38B1

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	1.798	50	97.1	0.055	26.33	2.3		73010

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	1.8	1.86			0.261

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.798	33.529	73009	3707	96.79	0.188	0.1853	0.1939	0.231	0.2388	24.683

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]
0.002	-0.001	0.001	-0.011	0.002	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	21.153
r_dihedral_angle_6_deg	16.158
r_dihedral_angle_3_deg	14.852
r_dihedral_angle_1_deg	7.146
r_lrange_it	6.732
r_lrange_other	6.722
r_scangle_it	4.639
r_scangle_other	4.639
r_mcangle_other	3.434
r_mcangle_it	3.433
r_scbond_it	3.049
r_scbond_other	3.048
r_mcbond_it	2.353
r_mcbond_other	2.341
r_angle_refined_deg	1.568
r_angle_other_deg	0.519
r_symmetry_nbd_refined	0.27
r_nbd_refined	0.234
r_nbd_other	0.231
r_symmetry_xyhbond_nbd_refined	0.201
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.079
r_symmetry_xyhbond_nbd_other	0.033
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6288
Nucleic Acid Atoms	531
Solvent Atoms	349
Heterogen Atoms	41

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing