1RK2 | pdb_00001rk2

E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP, SOLVED IN SPACE GROUP P212121

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RKD	1RKD: RESIDUES 4-9, 44-93, 123-241 AND 254-309

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.8		CRYSTALS WERE GROWN IN THE PRESENCE OF 5 MM RIBOSE, 10 MM ADP, 0.05 MM ALF4 AND 15 MM NAF USING 8.8-15% PEG 4000, 0.25 M MGCL2 AND 20% MPD IN 0.1 M TRIS- HCL BUFFERED TO PH 4.8.

Crystal Properties
Matthews coefficient	Solvent content
2.2	33.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.201	α = 90
b = 62.492	β = 90
c = 337.8	γ = 90

Symmetry
Space Group	P 21 21 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	IMAGE PLATE	MARRESEARCH	BENT MIRROR	1998-05-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11		EMBL/DESY, HAMBURG	X11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.25	13	99.1	0.072	17	4		55979			26

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.25	2.29	98.8		0.291	3.9	4

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1RKD: RESIDUES 4-9, 44-93, 123-241 AND 254-309	2.25	13	55979	2815	99	0.228	0.21	0.265	0.21	RANDOM	24.4

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]
1.63			5.01		-6.64

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.4
c_angle_deg	1.4
c_improper_angle_d	0.81
c_bond_d	0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8972
Nucleic Acid Atoms
Solvent Atoms	409
Heterogen Atoms	172

Software

Software
Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling