8IDV

Crystal structure of Fic protein from Mycoplasma mycoides


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5NH2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62930.1 M MES, 22% PEG400
Crystal Properties
Matthews coefficientSolvent content
3.8467.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.6α = 90
b = 120.6β = 90
c = 165.4γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL10U20.9792SSRFBL10U2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
13.4995095.60.1530.1680.99810.5618.518055122.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.53.7188.70.9210.9660.7931.6211.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT3.544.1916231178799.630.221970.213730.29713RANDOM139.589
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]
2.411.22.41-7.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.387
r_long_range_B_refined22.4
r_long_range_B_other22.399
r_dihedral_angle_3_deg21.625
r_scangle_other18.36
r_mcangle_other17.956
r_mcangle_it17.955
r_dihedral_angle_4_deg17.256
r_mcbond_it12.11
r_mcbond_other12.106
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.387
r_long_range_B_refined22.4
r_long_range_B_other22.399
r_dihedral_angle_3_deg21.625
r_scangle_other18.36
r_mcangle_other17.956
r_mcangle_it17.955
r_dihedral_angle_4_deg17.256
r_mcbond_it12.11
r_mcbond_other12.106
r_scbond_it12.067
r_scbond_other12.066
r_dihedral_angle_1_deg8.552
r_angle_refined_deg1.581
r_angle_other_deg1.144
r_chiral_restr0.06
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6017
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms40

Software

Software
Software NamePurpose
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
PHENIXrefinement