1V9K | pdb_00001v9k

The crystal structure of the catalytic domain of pseudouridine synthase RluC from Escherichia coli

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	ammonium sulfate, HEPES, sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.725	α = 90
b = 96.725	β = 90
c = 86.884	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	ADSC QUANTUM 210		2003-10-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	0.97876, 0.97919, 0.98140	Photon Factory	AR-NW12A

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	2	20	98	0.062		13.7		35502

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.07	83.5

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2	20	35502	1583	100	0.21254	0.20917	0.27551	RANDOM	35.263

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]
-1.11	-0.56		-1.11		1.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.668
r_scangle_it	5.699
r_scbond_it	3.796
r_mcangle_it	2.151
r_angle_refined_deg	2.08
r_mcbond_it	1.242
r_nbd_refined	0.227
r_symmetry_vdw_refined	0.206
r_chiral_restr	0.182
r_xyhbond_nbd_refined	0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.668
r_scangle_it	5.699
r_scbond_it	3.796
r_mcangle_it	2.151
r_angle_refined_deg	2.08
r_mcbond_it	1.242
r_nbd_refined	0.227
r_symmetry_vdw_refined	0.206
r_chiral_restr	0.182
r_xyhbond_nbd_refined	0.17
r_symmetry_hbond_refined	0.147
r_bond_refined_d	0.022
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3614
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.