7VH4 | pdb_00007vh4

Crystal structure of oligoribonuclease of Escherichia coli

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IGI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	20 mM Sodium HEPES, pH 7.5, 0.25 M Sodium acetate, 25 % v/v PEG-3350

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.574	α = 90
b = 100.574	β = 90
c = 147.831	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	PSI JUNGFRAU 4M		2018-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.96863	ESRF	ID29

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	2.3	59.63	99.8	0.074	0.086	0.043	0.98	11.7	7.8		34389			54.922

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.38	98.6		0.533	0.615	0.299	2.9	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-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	2IGI	2.3	59.63	32650	1673	99.78	0.1963	0.1938	0.1972	0.2449	0.2416	RANDOM	55.092

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]
-2.77			-2.77		5.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.156
r_dihedral_angle_4_deg	20.549
r_dihedral_angle_3_deg	13.907
r_dihedral_angle_1_deg	6.952
r_angle_refined_deg	1.422
r_angle_other_deg	1.271
r_chiral_restr	0.065
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5705
Nucleic Acid Atoms
Solvent Atoms	181
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction