2REF

Crystal structure of the loading GNATL domain of CurA from Lyngbya majuscula soaked with malonyl-CoA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2REEApo CurA GNATL domain

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP277.15Mother liquor: 100 mM Bis-Tris pH 6.8, 100 mM NaCl, 1.5 M ammonium sulfate, 20% glycerol. Protein buffer: 20 mM Tris pH 7.9, 500 mM NaCl, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Crystal Properties
Matthews coefficientSolvent content
3.2862.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.886α = 90
b = 91.886β = 90
c = 139.486γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDK-B pair of biomorph mirrors for vertical and horizontal focusing2006-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B0.97939APS23-ID-B

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
12.7546.599.90.09410.69.718214182141160.3
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)
12.752.8599.90.5344.99.81800

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUTApo CurA GNATL domain2.7546.5181931819091499.80.210.2070.251RANDOM39.054
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]
0.130.070.13-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.381
r_dihedral_angle_3_deg16.645
r_dihedral_angle_4_deg14.216
r_dihedral_angle_1_deg5.59
r_scangle_it1.561
r_angle_refined_deg1.351
r_scbond_it0.915
r_mcangle_it0.562
r_nbtor_refined0.305
r_mcbond_it0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.381
r_dihedral_angle_3_deg16.645
r_dihedral_angle_4_deg14.216
r_dihedral_angle_1_deg5.59
r_scangle_it1.561
r_angle_refined_deg1.351
r_scbond_it0.915
r_mcangle_it0.562
r_nbtor_refined0.305
r_mcbond_it0.304
r_nbd_refined0.213
r_symmetry_vdw_refined0.175
r_xyhbond_nbd_refined0.126
r_symmetry_hbond_refined0.098
r_chiral_restr0.093
r_bond_refined_d0.008
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3310
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms102

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
PHASERphasing