6ABX

Crystal structure of citrate synthase (Msed_1522) from Metallosphaera sedula in complex with citrate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.2295800mM sodium phosphate monobasic/1200mM potassium phosphate dibasic, 0.1 M sodium acetate/acetic acid pH 4.2
Crystal Properties
Matthews coefficientSolvent content
2.2144.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.181α = 93.56
b = 53.522β = 105.73
c = 76.285γ = 102.16
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702017-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 7A (6B, 6C1)0.97934PAL/PLS7A (6B, 6C1)

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
11.772.8497.10.057223.579198
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)
11.71.730.263

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 REPLACEMENTTHROUGHOUT1VGP1.729.1575282391696.770.14610.14430.1803RANDOM21.068
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]
-0.20.890.110.680.43-0.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.459
r_dihedral_angle_4_deg19.468
r_dihedral_angle_3_deg14.261
r_dihedral_angle_1_deg5.987
r_angle_refined_deg1.688
r_angle_other_deg1.082
r_chiral_restr0.162
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.459
r_dihedral_angle_4_deg19.468
r_dihedral_angle_3_deg14.261
r_dihedral_angle_1_deg5.987
r_angle_refined_deg1.688
r_angle_other_deg1.082
r_chiral_restr0.162
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5918
Nucleic Acid Atoms
Solvent Atoms593
Heterogen Atoms44

Software

Software
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
MOLREPphasing