2A88

Crystal structure of A Pantothenate synthetase, apo enzyme in C2 space group


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MOPpdb entry 1MOP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293PEG 3000, glycerol, isopropanol, magnesium chloride, lithium sulfate, imidazole, pH 8.0, temperature 293K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.8757.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.818α = 90
b = 44.983β = 125.5
c = 82.136γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-D1.5418

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
11.75097.30.05921.33.33846138461-3-325.9
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)
11.71.7688.888.80.3722.82.83453

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1MOP1.7203844238442310897.360.1550.1550.1520.186RANDOM38.188
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]
-0.14-0.170.32-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.224
r_dihedral_angle_4_deg17.801
r_dihedral_angle_3_deg13.937
r_scangle_it7.875
r_scbond_it5.513
r_dihedral_angle_1_deg5.287
r_mcangle_it3.534
r_mcbond_it2.61
r_angle_refined_deg1.614
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.224
r_dihedral_angle_4_deg17.801
r_dihedral_angle_3_deg13.937
r_scangle_it7.875
r_scbond_it5.513
r_dihedral_angle_1_deg5.287
r_mcangle_it3.534
r_mcbond_it2.61
r_angle_refined_deg1.614
r_nbtor_refined0.311
r_nbd_refined0.215
r_symmetry_vdw_refined0.177
r_xyhbond_nbd_refined0.139
r_chiral_restr0.133
r_symmetry_hbond_refined0.103
r_bond_refined_d0.019
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2033
Nucleic Acid Atoms
Solvent Atoms287
Heterogen Atoms17

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
AMoREphasing