1Z85

Crystal structure of a predicted rna methyltransferase (tm1380) from thermotoga maritima msb8 at 2.12 A resolution

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	8	277	1.0M LiCl, 20.0% PEG-6000, 0.1M TRIS pH 8.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.652	α = 90
b = 82.473	β = 90
c = 106.264	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 210	KOHZU: Double Crystal Si(111)	2004-11-23	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	0.979694,1.019775,0.979478	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.12	29.32	99.5	0.071	9	3.6		33166

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.12	2.23		99.9	0.518	1.5	3.6

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-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.12	29.32	31467	1677	99.14	0.174	0.1735	0.171	0.222	RANDOM	39.697

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]
1.98			-1.28		-0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.747
r_dihedral_angle_4_deg	18.195
r_dihedral_angle_3_deg	15.776
r_scangle_it	7.934
r_dihedral_angle_1_deg	6.862
r_scbond_it	6.212
r_mcangle_it	3.478
r_mcbond_it	2.409
r_angle_refined_deg	1.644
r_angle_other_deg	0.909
r_mcbond_other	0.628
r_symmetry_vdw_other	0.366
r_nbd_refined	0.2
r_symmetry_hbond_refined	0.193
r_nbtor_refined	0.181
r_symmetry_vdw_refined	0.181
r_nbd_other	0.179
r_xyhbond_nbd_refined	0.154
r_chiral_restr	0.142
r_nbtor_other	0.086
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3331
Nucleic Acid Atoms
Solvent Atoms	291
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
CCP4	data scaling
SHELXD	phasing
autoSHARP	phasing