7E8N

Crystal structure of Type II citrate synthase (HyCS) from Hymenobacter sp. PAMC 26554


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4TVM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M sodium cacodylate, HCl (pH 6.5), 1 M sodium citrate tribasic
Crystal Properties
Matthews coefficientSolvent content
2.652.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.339α = 90
b = 166.168β = 90
c = 135.335γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2020-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 5C (4A)0.979PAL/PLS5C (4A)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.25099.80.073147.27.976885
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)
12.22.240.342

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 REPLACEMENTTHROUGHOUT4TVM2.241.5872970384899.580.19230.190.2351RANDOM46.798
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]
-0.71-3.764.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.673
r_dihedral_angle_4_deg16.014
r_dihedral_angle_3_deg15.835
r_dihedral_angle_1_deg7.185
r_angle_refined_deg1.572
r_angle_other_deg1.326
r_chiral_restr0.075
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.673
r_dihedral_angle_4_deg16.014
r_dihedral_angle_3_deg15.835
r_dihedral_angle_1_deg7.185
r_angle_refined_deg1.572
r_angle_other_deg1.326
r_chiral_restr0.075
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10051
Nucleic Acid Atoms
Solvent Atoms394
Heterogen Atoms39

Software

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