8Z62 | pdb_00008z62

Crystal structure of rRNA (uracil-C5)-methyltransferase from Pyrococcus horikoshii OT3

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-O58994-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	7.5	293	0.1 M HEPES sodium pH 7.5, 2% (v/v) PEG 400, 2.0 M ammounium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.32	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.89	α = 90
b = 96.61	β = 90
c = 122.4	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++	Vari Max	2023-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	3.2	96.61	100	0.224	0.239	0.083	0.986	8.3	8		18612

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.2	3.42		100	0.536	0.572	0.198	0.898		8.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	AF-O58994-F1	3.2	75.83	17639	928	100	0.17247	0.16916	0.1776	0.23723	0.2395	RANDOM	48.149

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]
-2.4			2.95		-0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.242
r_dihedral_angle_2_deg	9.88
r_dihedral_angle_1_deg	7.509
r_long_range_B_refined	7.293
r_long_range_B_other	7.293
r_scangle_other	4.882
r_mcangle_it	4.042
r_mcangle_other	4.042
r_scbond_it	2.882
r_scbond_other	2.881
r_mcbond_it	2.434
r_mcbond_other	2.434
r_angle_refined_deg	1.407
r_angle_other_deg	0.434
r_chiral_restr	0.056
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6610
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms	59

Software

Software
Software Name	Purpose
HKL-3000	data collection
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction