3HEE | pdb_00003hee

Structural study of Clostridium thermocellum Ribose-5-Phosphate Isomerase B and ribose-5-phosphate

X-RAY DIFFRACTION

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, HANGING DROP	7	283	0.05M Tris, pH7.0, 10% PEG8000, 0.15M Magnesium chloride, 0.2M Potassium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 283K

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.381	α = 90
b = 69.381	β = 90
c = 153.566	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	2	50	98.3	0.095	0.095	31.6	16.3		29281	1.3	1.2	25.1

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)
	2	50	98.3		0.095	0.095	31.6	16.3	29281

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-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	2	33.84	27713	1487	98.23	0.17668	0.17433	0.18	0.22051	0.22	RANDOM	25.078

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]
					-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.281
r_dihedral_angle_4_deg	18.438
r_dihedral_angle_3_deg	13.511
r_dihedral_angle_1_deg	6.036
r_scangle_it	5.877
r_scbond_it	4.113
r_mcangle_it	2.241
r_angle_refined_deg	2.192
r_mcbond_it	1.62
r_symmetry_hbond_refined	0.435

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.281
r_dihedral_angle_4_deg	18.438
r_dihedral_angle_3_deg	13.511
r_dihedral_angle_1_deg	6.036
r_scangle_it	5.877
r_scbond_it	4.113
r_mcangle_it	2.241
r_angle_refined_deg	2.192
r_mcbond_it	1.62
r_symmetry_hbond_refined	0.435
r_nbtor_refined	0.305
r_nbd_refined	0.215
r_chiral_restr	0.174
r_xyhbond_nbd_refined	0.14
r_symmetry_vdw_refined	0.13
r_bond_refined_d	0.032
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2244
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	28

Software

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

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.