3HE8 | pdb_00003he8

Structural study of Clostridium thermocellum Ribose-5-Phosphate Isomerase B

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VVR	PDB ENTRY 2VVR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	283	0.05M Tris, pH7.0, 10% PEG8000, 0.15M Magnesium chloride, 0.2M Potassium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 283K

Crystal Properties
Matthews coefficient	Solvent content
3.33	63.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.515	α = 90
b = 69.515	β = 90
c = 154.434	γ = 120

Symmetry
Space Group	P 32 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	CCD	ADSC QUANTUM 210		2008-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 6C1	0.9999	PAL/PLS	6C1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.9	50	92.2	0.035	0.051	63.1	21.1		32228	1.7	1.3	25.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	50	92.2		0.051	0.051	63.1	21.1	32228

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2VVR	1.9	28.81	1.3	1.7	32228	30510	1630	92.15	0.18924	0.18763	0.1878	0.22011	0.218	RANDOM	25.936

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
r_dihedral_angle_2_deg	36.262
r_dihedral_angle_4_deg	18.707
r_dihedral_angle_3_deg	12.696
r_dihedral_angle_1_deg	5.298
r_scangle_it	3.769
r_scbond_it	2.525
r_mcangle_it	1.378
r_angle_refined_deg	1.332
r_mcbond_it	0.875
r_nbtor_refined	0.301
r_nbd_refined	0.203
r_symmetry_vdw_refined	0.15
r_xyhbond_nbd_refined	0.141
r_symmetry_hbond_refined	0.124
r_chiral_restr	0.09
r_bond_refined_d	0.015
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2244
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	12

Software

Software
Software Name	Purpose
HKL-2000	data collection
swiss-model	model building
REFMAC	refinement
swiss-model	phasing