2C8B

Structure of the ARTT motif Q212A mutant C3bot1 Exoenzyme (Free state, crystal form II)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GZFPDB ENTRY 1GZF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
122.5% PEG 3350 W/W, 100 MM LI2SO4, 100 MM SODIUM CITRATE PH 3.0, 3-10% MPEG 550 V/V
Crystal Properties
Matthews coefficientSolvent content
2.0339.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.941α = 90
b = 86.884β = 117.31
c = 42.896γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

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
11.747.141000.0317.25.5918292

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 1GZF1.747.142122711441000.1920.1910.218RANDOM17.34
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]
1.38-0.07-0.94-0.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.461
r_scangle_it2.953
r_scbond_it1.666
r_angle_refined_deg1.048
r_mcangle_it1.031
r_angle_other_deg0.722
r_mcbond_it0.505
r_nbd_other0.234
r_symmetry_vdw_other0.232
r_symmetry_vdw_refined0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.461
r_scangle_it2.953
r_scbond_it1.666
r_angle_refined_deg1.048
r_mcangle_it1.031
r_angle_other_deg0.722
r_mcbond_it0.505
r_nbd_other0.234
r_symmetry_vdw_other0.232
r_symmetry_vdw_refined0.19
r_nbd_refined0.189
r_symmetry_hbond_refined0.15
r_xyhbond_nbd_refined0.127
r_nbtor_other0.078
r_chiral_restr0.06
r_gen_planes_refined0.009
r_bond_refined_d0.006
r_bond_other_d0.006
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1578
Nucleic Acid Atoms
Solvent Atoms229
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing