1RKA

THE APO FORM OF E. COLI RIBOKINASE

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 22-33% PEG 2000, MONO-METHYLETHER AS PRECIPITANT AND BUFFERED TO PH 4.8 WITH 0.1 M NA ACETATE. CRYO-PROTECTANT: MOTHER LIQUID ALSO CONTAINING 15% ETHYLENEGLYCOL. SOAK-TIME: 2-3 MINUTES.

Crystal Properties
Matthews coefficient	Solvent content
2.1	40.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.97	α = 90
b = 61.97	β = 90
c = 127.834	γ = 120

Symmetry
Space Group	P 31 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	100	IMAGE PLATE	MARRESEARCH	MIRRORS	1998-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I711		MAX II	I711

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	2.3	15	96.4	0.056	20.6	5.5		12644			32

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)
1	2.3	2.34	87.5		0.235	6.7	5.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1RKD: RESIDUES 4-9, 44-93, 123-241 AND 254-309.	2.3	15	12644	12644	619	96.3	0.21	0.253	RANDOM	27

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]
-2.84	-1.66		-2.84		5.685

RMS Deviations
Key	Refinement Restraint Deviation
x_dihedral_angle_d	23.1
x_scangle_it	2.5
x_scbond_it	1.8
x_mcangle_it	1.7
x_angle_deg	1.5
x_mcbond_it	1.1
x_improper_angle_d	0.76
x_bond_d	0.007
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	2236
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms

Software

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