3FUV | pdb_00003fuv

Apo-form of T. thermophilus 16S rRNA A1518 and A1519 methyltransferase (KsgA) in space group P43212

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	microbatch technique under oil	8.5	277	160 mM magnesium chloride hexahydrate, 80 mM TRIS (pH 8.5), 24% w/v polyethylene glycol 4000 and 20% v/v anhydrous glycerol, microbatch technique under oil, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.111	α = 90
b = 85.111	β = 90
c = 215.867	γ = 90

Symmetry
Space Group	P 43 21 2

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	MAR CCD 130 mm	Bent single Si (111) crystal monochromator (horizontal focusing and deflection) with vertical focusing mirror			SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4C	0.9797	NSLS	X4C

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	1.95	30	99.9	0.086	29.8	11.8		59133

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	1.95	2	100		0.42	3.36	7.9	5776

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1.95	25	58998	2986	99.86	0.233	0.229	0.2279	0.309	0.3026	RANDOM	38.071

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]
-0.47			-0.47		0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.272
r_dihedral_angle_4_deg	19.071
r_dihedral_angle_3_deg	18.934
r_dihedral_angle_1_deg	7.084
r_scangle_it	4.702
r_scbond_it	3.128
r_angle_refined_deg	2.096
r_mcangle_it	1.903
r_mcbond_it	1.301
r_nbtor_refined	0.313
r_symmetry_vdw_refined	0.3
r_symmetry_hbond_refined	0.247
r_nbd_refined	0.241
r_xyhbond_nbd_refined	0.203
r_chiral_restr	0.145
r_bond_refined_d	0.024
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5995
Nucleic Acid Atoms
Solvent Atoms	568
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling