2FN9 | pdb_00002fn9

Thermotoga maritima Ribose Binding Protein Unliganded Form

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	5.9	290	0.2M NaCl, 0.1M Bis-Tris pH5.9, 25% PEG 3350, MICRO-BATCH, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.901	α = 90
b = 136.826	β = 90
c = 144.465	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	CCD	MARMOSAIC 300 mm CCD		2005-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.997	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.4	50	99	0.05		5.8	115461	115461

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.45	91.4	91.4	0.515	1.7	3.4

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	PDB ENTRY 2DRI	1.4	50	115460	115460	5767	98.97	0.181	0.181	0.18	0.18	0.203	0.2	RANDOM	14.532

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]
-0.42			0.38		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.25
r_dihedral_angle_4_deg	17.466
r_dihedral_angle_3_deg	12.6
r_dihedral_angle_1_deg	5.223
r_scangle_it	2.914
r_scbond_it	2.144
r_angle_refined_deg	1.199
r_mcangle_it	1.119
r_mcbond_it	1.052
r_angle_other_deg	0.755
r_symmetry_vdw_other	0.237
r_nbd_refined	0.208
r_nbtor_refined	0.184
r_nbd_other	0.174
r_mcbond_other	0.173
r_symmetry_vdw_refined	0.138
r_symmetry_hbond_refined	0.135
r_xyhbond_nbd_refined	0.131
r_nbtor_other	0.082
r_chiral_restr	0.073
r_xyhbond_nbd_other	0.047
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4362
Nucleic Acid Atoms
Solvent Atoms	627
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
AMoRE	phasing