1O5I

Crystal structure of 3-oxoacyl-(acyl carrier protein) reductase (TM1169) from Thermotoga maritima at 2.50 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1I01 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP529320% PEG-6000, 0.1M citric acid pH 5.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5451.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.515α = 90
b = 117.12β = 90
c = 140.847γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315flat mirror2002-01-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-1SSRLBL11-1

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
12.541.1785.40.127.72.5316333163351.32
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)
12.52.6442.70.2291.61.42231

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 DIFFRACTIONSAD, MOLECULAR REPLACEMENTTHROUGHOUT1i012.541.1730035156285.030.196620.194040.2468RANDOM15.52
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]
-1.87-6.168.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.365
r_dihedral_angle_4_deg22.795
r_dihedral_angle_3_deg20.263
r_dihedral_angle_1_deg6.747
r_scangle_it2.774
r_angle_refined_deg1.755
r_scbond_it1.648
r_mcangle_it1.216
r_angle_other_deg0.944
r_mcbond_it0.705
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.365
r_dihedral_angle_4_deg22.795
r_dihedral_angle_3_deg20.263
r_dihedral_angle_1_deg6.747
r_scangle_it2.774
r_angle_refined_deg1.755
r_scbond_it1.648
r_mcangle_it1.216
r_angle_other_deg0.944
r_mcbond_it0.705
r_symmetry_hbond_refined0.487
r_symmetry_vdw_other0.312
r_symmetry_vdw_refined0.241
r_nbd_refined0.204
r_nbd_other0.189
r_chiral_restr0.095
r_nbtor_other0.089
r_xyhbond_nbd_refined0.031
r_bond_refined_d0.018
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7165
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms35

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
CCP4data scaling