1RKD | pdb_00001rkd

E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.4		CRYSTALS WERE GROWN IN THE PRESENCE OF 0.5 MM RIBOSE, 10 MM AMP-PNP AND 10 MM MGCL2 USING 2.1-2.4 M NH4H2PO4 AS PRECIPITANT AND BUFFERED TO PH 8.4 WITH 0.1 M TRIS-HCL.

Crystal Properties
Matthews coefficient	Solvent content
3.1	49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.4	α = 90
b = 95.4	β = 90
c = 154.87	γ = 120

Symmetry
Space Group	P 61 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	IMAGE PLATE	MARRESEARCH		1996-11-30	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B		EMBL/DESY, HAMBURG	BW7B

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	1.84	30	95.5	0.055	30.2	7.5		35015			23

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	1.84	1.87	97.8		0.239	7.4	7.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MULTIPLE ISOMORPHOUS REPLACEMENT	THROUGHOUT	1.84	28	35013	3542	95.5	0.221	0.22	0.2	0.258	0.21	RANDOM	29

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
p_transverse_tor	29.6
p_staggered_tor	16.2
p_scangle_it	5
p_planar_tor	4.2
p_scbond_it	3.5
p_mcangle_it	2
p_mcbond_it	1.4
p_multtor_nbd	0.25
p_singtor_nbd	0.18
p_xyhbond_nbd	0.15
p_chiral_restr	0.13
p_planar_d	0.033
p_angle_d	0.028
p_plane_restr	0.02
p_bond_d	0.013
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2248
Nucleic Acid Atoms
Solvent Atoms	181
Heterogen Atoms	47

Software

Software
Software Name	Purpose
MLPHARE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling