4DHD

Crystal structure of isoprenoid synthase A3MSH1 (TARGET EFI-501992) from Pyrobaculum calidifontis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WY0PDB ENTRY 1WY0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.50.1M BIS-TRIS, 25% PEG3350, PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294
Crystal Properties
Matthews coefficientSolvent content
2.5652.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.401α = 90
b = 89.269β = 90
c = 149.542γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2011-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

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
11.657093.80.1179.97.749409-522.442
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)
11.651.681000.363.88

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1WY01.655044552143093.070.181620.180620.21252RANDOM27.387
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]
2.27-1.65-0.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.446
r_dihedral_angle_4_deg14.586
r_dihedral_angle_3_deg12.073
r_dihedral_angle_1_deg4.26
r_angle_refined_deg1.26
r_chiral_restr0.075
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.446
r_dihedral_angle_4_deg14.586
r_dihedral_angle_3_deg12.073
r_dihedral_angle_1_deg4.26
r_angle_refined_deg1.26
r_chiral_restr0.075
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2564
Nucleic Acid Atoms
Solvent Atoms316
Heterogen Atoms10

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling