2FCL

Crystal structure of a putative nucleotidyltransferase (tm1012) from Thermotoga maritima at 1.35 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2EWRpdb entry 2ewr

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP, NANODROP5.627715.0% Glycerol, 0.17M NH4OAc, 25.5% PEG-4000, 0.1M Citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1843.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.769α = 73.69
b = 36.382β = 85.51
c = 39.785γ = 78.97
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Flat mirror (vertical focusing)2005-04-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.979454SSRLBL11-1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.225.8873.50.0340.03420.32.33982711.7
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)RedundancyNumber Unique Reflections (All)
1.21.2317.60.1460.1465.72

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 REPLACEMENTTHROUGHOUTpdb entry 2ewr1.224.2837613202874.770.1420.140.17RANDOM13.634
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]
-0.770.31-0.17-0.240.220.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.504
r_dihedral_angle_4_deg12.17
r_dihedral_angle_3_deg10.994
r_dihedral_angle_1_deg5.901
r_scangle_it4.992
r_sphericity_bonded4.336
r_scbond_it3.749
r_mcangle_it2.872
r_mcbond_it2.188
r_rigid_bond_restr2.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.504
r_dihedral_angle_4_deg12.17
r_dihedral_angle_3_deg10.994
r_dihedral_angle_1_deg5.901
r_scangle_it4.992
r_sphericity_bonded4.336
r_scbond_it3.749
r_mcangle_it2.872
r_mcbond_it2.188
r_rigid_bond_restr2.002
r_mcbond_other1.445
r_angle_refined_deg1.335
r_angle_other_deg0.785
r_symmetry_vdw_other0.257
r_nbd_refined0.237
r_xyhbond_nbd_refined0.207
r_nbd_other0.189
r_nbtor_refined0.183
r_symmetry_hbond_refined0.141
r_chiral_restr0.082
r_nbtor_other0.082
r_symmetry_vdw_refined0.078
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1308
Nucleic Acid Atoms
Solvent Atoms261
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling