1VM7

Crystal structure of Ribokinase (TM0960) from Thermotoga maritima at 2.15 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GQT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP2930.4M (NH4)2Tartrate, 0.4% PEG-3350, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3447.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 181.142α = 90
b = 45.265β = 93.3
c = 77.26γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC2004-02-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.3ALS5.0.3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1260.492.30.07103.23937537.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0561.20.6821.31.91884

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1gqt2.1560.432122167697.960.191890.189540.23539RANDOM31.282
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]
1.990.85-1.2-0.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.216
r_dihedral_angle_4_deg21.355
r_dihedral_angle_3_deg14.158
r_dihedral_angle_1_deg6.023
r_scangle_it2.376
r_scbond_it1.559
r_angle_refined_deg1.477
r_angle_other_deg0.862
r_mcangle_it0.839
r_mcbond_it0.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.216
r_dihedral_angle_4_deg21.355
r_dihedral_angle_3_deg14.158
r_dihedral_angle_1_deg6.023
r_scangle_it2.376
r_scbond_it1.559
r_angle_refined_deg1.477
r_angle_other_deg0.862
r_mcangle_it0.839
r_mcbond_it0.55
r_symmetry_hbond_refined0.254
r_nbd_refined0.202
r_symmetry_vdw_other0.186
r_nbtor_refined0.181
r_xyhbond_nbd_refined0.178
r_nbd_other0.177
r_symmetry_vdw_refined0.16
r_mcbond_other0.16
r_nbtor_other0.087
r_chiral_restr0.081
r_xyhbond_nbd_other0.059
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4537
Nucleic Acid Atoms
Solvent Atoms279
Heterogen Atoms

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
CCP4data scaling