2C4B

Inhibitor cystine knot protein McoEeTI fused to the catalytically inactive barnase mutant H102A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1A2PPDB ENTRY 1A2P

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2771.3 M AMMONIUM SULPHATE, 7% PEG400 (V/V), 0.1 M MES PH 6.5 AS RESERVOIR SOLUTION. DROPLETS MIXED FROM 8 UL PROTEIN (30 MG/ML) AND 4 UL RESERVOIR. SITTING DROP VAPOR DIFFUSION. 4 DEG. C.
Crystal Properties
Matthews coefficientSolvent content
3.867

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.02α = 90
b = 217.71β = 90
c = 58.34γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-05-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW6MPG/DESY, HAMBURGBW6

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
11.339.898.70.04143.1114401-319.5
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)
11.31.498.10.422.422.7

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 1A2P1.339.8411210822911000.1330.1320.164RANDOM17.55
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]
0.93-0.6-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.631
r_dihedral_angle_4_deg18.483
r_scangle_it12.789
r_dihedral_angle_3_deg11.118
r_scbond_it10.018
r_dihedral_angle_1_deg6.646
r_mcangle_it5.214
r_mcbond_it4.582
r_angle_refined_deg2.319
r_angle_other_deg1.657
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.631
r_dihedral_angle_4_deg18.483
r_scangle_it12.789
r_dihedral_angle_3_deg11.118
r_scbond_it10.018
r_dihedral_angle_1_deg6.646
r_mcangle_it5.214
r_mcbond_it4.582
r_angle_refined_deg2.319
r_angle_other_deg1.657
r_chiral_restr0.348
r_symmetry_vdw_other0.29
r_symmetry_vdw_refined0.285
r_nbd_other0.224
r_nbd_refined0.223
r_nbtor_refined0.188
r_xyhbond_nbd_refined0.182
r_symmetry_hbond_refined0.159
r_nbtor_other0.096
r_bond_refined_d0.021
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms2188
Nucleic Acid Atoms
Solvent Atoms509
Heterogen Atoms218

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
EPMRphasing