3BB7

Structure of Prevotella intermedia prointerpain A fragment 39-359 (mutant C154A)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DKIPDB entry 1DKI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529310% polyethylene glycol 3000, 0.2M magnesium chloride, 0.1M sodium cacodylate, pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2244.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.87α = 90
b = 38.81β = 127.26
c = 78.14γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-09-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9763ESRFID29

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
11.539.0799.50.0816.4749377493771.513.9
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)
11.51.5897.40.4095.36.1

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 1DKI1.539.07486304863074799.510.15560.15560.155020.19338RANDOM15.895
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]
-0.130.220.42-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.017
r_dihedral_angle_4_deg16.445
r_dihedral_angle_3_deg13.159
r_dihedral_angle_1_deg5.266
r_scangle_it3.877
r_sphericity_bonded2.926
r_scbond_it2.803
r_mcangle_it1.986
r_rigid_bond_restr1.57
r_angle_refined_deg1.399
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.017
r_dihedral_angle_4_deg16.445
r_dihedral_angle_3_deg13.159
r_dihedral_angle_1_deg5.266
r_scangle_it3.877
r_sphericity_bonded2.926
r_scbond_it2.803
r_mcangle_it1.986
r_rigid_bond_restr1.57
r_angle_refined_deg1.399
r_mcbond_it1.36
r_nbtor_refined0.313
r_symmetry_vdw_refined0.227
r_nbd_refined0.196
r_symmetry_hbond_refined0.175
r_xyhbond_nbd_refined0.148
r_chiral_restr0.1
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_sphericity_free
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2428
Nucleic Acid Atoms
Solvent Atoms370
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing