1SGV

STRUCTURE OF TRNA PSI55 PSEUDOURIDINE SYNTHASE (TRUB)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1K8W	PDB entry 1K8W protein component

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	microseeding	7.5	298	AMMONIUM SULFATE, TRIS BUFFER, PEG3350, pH 7.5, temperature 298K, microseeding

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.948	α = 90
b = 94.1	β = 100.36
c = 78.508	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	ADSC QUANTUM 4			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	1.0322	ALS	5.0.1

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	1.9	40.2		0.046	12.4	3.6		51411			28.8

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	1.9	1.97			0.34	2	3.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1K8W protein component	1.9	40.16	48859	2551	99.43	0.20268	0.20082	0.23947	RANDOM	20.756

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]
-0.04		0.35	-0.43		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.461
r_scangle_it	2.258
r_scbond_it	1.254
r_angle_refined_deg	0.973
r_mcangle_it	0.749
r_mcbond_it	0.387
r_symmetry_vdw_refined	0.191
r_nbd_refined	0.183
r_symmetry_hbond_refined	0.144
r_xyhbond_nbd_refined	0.127
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3930
Nucleic Acid Atoms
Solvent Atoms	451
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing