8YYK | pdb_00008yyk

Structure of RNase J2 wild type at room temperature

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6K6W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	5.6	291	100mM tri-sodium citrate dihydrate pH 5.6, 20% PEG 4000, 20% Isopropanol, 40% Formamide

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.304	α = 90
b = 133.38	β = 92.019
c = 117.751	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	278	IMAGE PLATE	RIGAKU RAXIS IV		2022-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU R-AXIS IV	1.541

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	58.6	90.1	0.19	0.92	4.6	2.6		29972

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.2	3.37			0.6	0.48

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3.2	58.6	29951	1392	89.671	0.207	0.2049	0.2079	0.2477	0.2471	38.488

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]
0.354		-0.024	0.568		-0.918

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.212
r_dihedral_angle_3_deg	14.696
r_dihedral_angle_2_deg	10.107
r_lrange_it	9.404
r_lrange_other	9.404
r_dihedral_angle_1_deg	6.413
r_mcangle_it	4.222
r_mcangle_other	4.222
r_scangle_it	3.995
r_scangle_other	3.995
r_scbond_it	2.456
r_scbond_other	2.456
r_mcbond_it	2.446
r_mcbond_other	2.442
r_angle_refined_deg	1.118
r_angle_other_deg	0.368
r_symmetry_nbd_refined	0.332
r_nbd_other	0.33
r_nbd_refined	0.207
r_symmetry_nbd_other	0.204
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.151
r_symmetry_xyhbond_nbd_refined	0.147
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.04
r_symmetry_xyhbond_nbd_other	0.023
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13034
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing