2IOY | pdb_00002ioy

Crystal structure of Thermoanaerobacter tengcongensis ribose binding protein

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4	290	0.1M Na Citrate, pH 4.0, 0.1M Potassium Phosphate Mono-Basic, 50% PEG1000, Micro-batch, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.18	α = 90
b = 35.8	β = 107.02
c = 118.03	γ = 90

Symmetry
Space Group	C 1 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	MARMOSAIC 225 mm CCD		2005-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.0	APS	22-BM

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	15	96	0.08	0.08	7.7	3.3	37592	37592

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)
	1.9	2	95.1		0.324	0.324	1.9	3.1	5405

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.9	15	37592	37592	1890	95.43	0.201	0.201	0.199	0.21	0.234	0.24	RANDOM	15.876

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]
		0.26	0.53		-0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.348
r_dihedral_angle_4_deg	14.545
r_dihedral_angle_3_deg	12.419
r_dihedral_angle_1_deg	6.048
r_scangle_it	2.914
r_scbond_it	1.978
r_angle_refined_deg	1.221
r_mcangle_it	1.163
r_angle_other_deg	0.928
r_mcbond_it	0.799
r_symmetry_vdw_refined	0.223
r_nbd_refined	0.211
r_symmetry_vdw_other	0.196
r_nbd_other	0.181
r_symmetry_hbond_refined	0.178
r_nbtor_refined	0.165
r_mcbond_other	0.156
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.126
r_nbtor_other	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4265
Nucleic Acid Atoms
Solvent Atoms	346
Heterogen Atoms	20

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
CCP4	data scaling
AMoRE	phasing