1VL4 | pdb_00001vl4

CRYSTAL STRUCTURE OF A PUTATIVE MODULATOR OF A DNA GYRASE (TM0727) FROM THERMOTOGA MARITIMA MSB8 AT 1.95 A RESOLUTION


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP7277TRIS pH 7, 0.5M (NH4)2SO4, 10% Glycerol, 30% PEG-600 , pH 7.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
2VAPOR DIFFUSION,SITTING DROP,NANODROP72770.5M (NH4)2SO4, 10% Glycerol, 30% PEG-600, TRIS pH 7, pH 7.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5952.46
2.5751.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.367α = 90
b = 106.637β = 90
c = 120.382γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152004-04-15MSINGLE WAVELENGTH
21x-ray100CCDADSC QUANTUM 315flat mirror2004-05-24MMAD
1,21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-2SSRLBL9-2
2SYNCHROTRONSSRL BEAMLINE BL11-10.979264,0.979562,0.898404SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
1,21.9548.7594.40.09211.53.87156732.71
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1,21.95256.30.4581.72.73069

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT1.9548.7567979358494.050.176280.173890.180.220990.23RANDOM16.661
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]
-0.340.41-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.814
r_dihedral_angle_4_deg17.466
r_dihedral_angle_3_deg14.752
r_scangle_it8.817
r_dihedral_angle_1_deg6.705
r_scbond_it6.278
r_mcangle_it3.624
r_mcbond_it2.706
r_angle_refined_deg1.669
r_angle_other_deg0.833
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6596
Nucleic Acid Atoms
Solvent Atoms493
Heterogen Atoms

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
SOLOMONphasing
REFMACrefinement
CCP4data scaling