4GMA | pdb_00004gma

Crystal structure of the adenosylcobalamin riboswitch

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop	7.5	298	10% isopropanol, 300 mM magnesium chloride, 100 mM sodium HEPES pH 7.5, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
4.1	69.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.648	α = 90
b = 243.545	β = 90
c = 87.102	γ = 90

Symmetry
Space Group	C 2 2 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	ADSC QUANTUM 315r			M	SINGLE WAVELENGTH
2	1
3	1
4	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	0.97	ALS	5.0.2

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	3.94	88.374	99.4	0.048	13.7	3.5		8706

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	4.64	4.89	99.9		0.498	0.498	1.6	3.6	855

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	MIR	THROUGHOUT	3.94	42.26	9479	8706	411	92.23	0.2622	0.2628	0.2622	0.2835	0.2752	0.3026	RANDOM	220.6988

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]
-5.762			-23.219		28.981

RMS Deviations
Key	Refinement Restraint Deviation
c_mcangle_it	38.739
c_mcbond_it	30.189
c_angle_d	0.867
c_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	4140
Solvent Atoms
Heterogen Atoms	109

Software

Software
Software Name	Purpose
SCALA	data scaling
BUSTER-TNT	refinement
SHARP	phasing
PDB_EXTRACT	data extraction
XDS	data reduction