4RSK | pdb_00004rsk

STRUCTURE OF THE K7A/R10A/K66A VARIANT OF RIBONUCLEASE A COMPLEXED WITH 3'-UMP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3RSK	PDB ENTRY 3RSK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5		CRYSTALS WERE PREPARED USING THE HANGING DROP METHOD. LYOPHILIZED K7A/R10A/K66A RNASE A WAS DISSOLVED IN UNBUFFERED WATER TO A CONCENTRATION OF 60MG/ML. DROPS CONSISTING OF PROTEIN SOLUTION (1.5MICROLITER), WATER (1.5MICROLITER), AND RESERVOIR SOLUTION (3.0MICROLITER) WERE SUSPENDED OVER 0.5 ML OF RESERVOIR SOLUTION (0.1M SODIUM ACETATE BUFFER, PH 4.5, CONTAINING 36% PEG 4000). THE COMPLEX WITH 3'-UMP WAS PREPARED BY SOAKING CRYSTALS IN MOTHER LIQUOR CONTAINING 5MM 3'-UMP FOR 2 DAYS., vapor diffusion - hanging drop

Crystal Properties
Matthews coefficient	Solvent content
3.47	60

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.62	α = 90
b = 69.62	β = 90
c = 66.98	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	273	AREA DETECTOR	SIEMENS	LONG MIRRORS	1997-09-12	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.1	30	88	0.026	19.8	2.4		33552		0.33

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	2.2	88		0.12

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	DIFFERENCE FOURIER	PDB ENTRY 3RSK	2.1	30	14210	14210		88	0.168

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]

RMS Deviations
Key	Refinement Restraint Deviation
t_dihedral_angle_d	17.475
t_angle_deg	2.208
t_it	1
t_nbd	0.018
t_bond_d	0.011
t_gen_planes	0.011
t_trig_c_planes	0.006
t_incorr_chiral_ct
t_pseud_angle

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	937
Nucleic Acid Atoms
Solvent Atoms	94
Heterogen Atoms	21

Software

Software
Software Name	Purpose
XDS	data scaling
XCALIBRE	data reduction
TNT	refinement
XDS	data reduction
XCALIBRE	data scaling
TNT	phasing