8SSF | pdb_00008ssf

Minimal protein-only/RNA-free Ribonuclease P from Hydrogenobacter thermophilus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7F3E
experimental model	PDB	7OG5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	277.15	2 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.92	57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.579	α = 90
b = 109.214	β = 90
c = 106.152	γ = 90

Symmetry
Space Group	C 2 2 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	PIXEL	DECTRIS EIGER X 16M		2020-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.03317	APS	23-ID-B

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	2.5	69.72	100	0.304	0.324	0.111	0.991	6.3	8.6		18589

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	2.5	2.6		100	4.001	4.26	1.443	0.434		8.8

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7F3E	2.5	69.72	18563	964	100	0.2	0.2071	0.244	0.25	70.31

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]
5.538			-0.474		-5.063

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	18.365
r_scangle_other	18.311
r_dihedral_angle_3_deg	17.99
r_scbond_it	13.231
r_scbond_other	13.212
r_mcangle_it	11.467
r_mcangle_other	11.467
r_dihedral_angle_2_deg	9.306
r_mcbond_it	9.097
r_mcbond_other	9.089
r_dihedral_angle_1_deg	4.386
r_angle_refined_deg	1.9
r_angle_other_deg	0.57
r_nbd_other	0.226
r_nbd_refined	0.214
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.132
r_chiral_restr	0.09
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbtor_other
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_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2897
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
DIALS	data reduction
DIALS	data scaling