4JYA | pdb_00004jya

Crystal structures of pseudouridinilated stop codons with ASLs

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	6.5	277.15	12% MPD, 0.1M MES-KOH, 0.075M magnesium chloride, 0.1M KCL, pH 6.5, EVAPORATION, temperature 277.15K

Crystal Properties
Matthews coefficient	Solvent content
4.6	73.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 402.32	α = 90
b = 402.32	β = 90
c = 174.93	γ = 90

Symmetry
Space Group	P 41 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	277	CCD	ADSC QUANTUM 315r		2012-08-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	1.000	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.098	48.93	98.95			242068	254809	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.098	3.178	98.33

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	MOLECULAR REPLACEMENT	THROUGHOUT	3.098	48.93	254809	254809	12741	98.95	0.1853	0.1853	0.1829	0.1835	0.2318	0.232	RANDOM	83.7225

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.992
r_dihedral_angle_3_deg	24.456
r_dihedral_angle_4_deg	19.538
r_mcangle_it	10.964
r_dihedral_angle_1_deg	8.494
r_mcbond_it	6.927
r_scbond_it	6.68
r_angle_refined_deg	1.748
r_chiral_restr	0.121
r_bond_refined_d	0.009
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19120
Nucleic Acid Atoms	32911
Solvent Atoms
Heterogen Atoms	56

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
XDS	data scaling
MOLREP	phasing