4Q0P | pdb_00004q0p

Crystal structure of Acinetobacter sp. DL28 L-ribose isomerase in complex with L-ribose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		The structure model of selenomethione derivative solved by MAD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	10-16%(v/v) PEG400, 0.2M NaCl, 0.1M HEPES, 0.02M Hexaammine cobalt(III) chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.38	α = 90
b = 107.93	β = 90
c = 119.41	γ = 90

Symmetry
Space Group	F 2 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	100	IMAGE PLATE	RIGAKU RAXIS VII	Mirrors	2011-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	1.93	20.5	99.7	0.052	12.1	3.2	23208	23208			24.2

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	1.93	2	99.6		0.278	3.8	3.1	2294

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-Factor (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	The structure model of selenomethione derivative solved by MAD	1.93	20.49	23208	23208	2288	99.5	0.211	0.208	0.208	0.2	0.242	0.23	RANDOM	36.6

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]
-4.98			-4.67		9.64

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	25.3
c_scangle_it	2.69
c_mcangle_it	2.28
c_scbond_it	1.86
c_angle_deg	1.4
c_mcbond_it	1.39
c_improper_angle_d	0.9
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1930
Nucleic Acid Atoms
Solvent Atoms	143
Heterogen Atoms	48

Software

Software
Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
CNS	refinement
CrystalClear	data reduction
CrystalClear	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.