1AFK | pdb_00001afk

CRYSTAL STRUCTURE OF RIBONUCLEASE A IN COMPLEX WITH 5'-DIPHOSPHOADENOSINE-3'-PHOSPHATE

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3RN3	PDB ENTRY 3RN3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5	289	PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, 20 MM SODIUM CITRATE, PH 5.5 AND THEN SOAKED WITH 1MM 5' DIPHOSPHOADENOSINE 3'-PHOSPHATE FOR 2.5 HRS AT 16 C, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.2	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.54	α = 90
b = 33.36	β = 90.09
c = 73.25	γ = 90

Symmetry
Space Group	C 1 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	293	IMAGE PLATE	MARRESEARCH		1995-07-17	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X31		EMBL/DESY, HAMBURG	X31

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	1.7	30	91.4	0.057	9.2	3		24687			18.7

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)
	1.7	1.77	82.4		0.339	1.95	1.8

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3RN3	1.7	8	24566	1189	90.4	0.211	0.211	0.266	RANDOM	22.3

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
x_dihedral_angle_d	25
x_scangle_it	4.01
x_mcangle_it	2.62
x_scbond_it	2.54
x_mcbond_it	1.56
x_angle_deg	1.4
x_improper_angle_d	1.22
x_bond_d	0.009
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1902
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms	62

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement