1W74

X-ray structure of peptidyl-prolyl cis-trans isomerase A, PpiA, Rv0009, from Mycobacterium tuberculosis.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16PROTEIN WAS CO-CRYSTALLIZED WITH THE PEPTIDE HAGPIA (FINAL CONCENTRATION 1 MM) FROM 30% PEG-200, 5% PEG-3000, 0.1 M MES-HCL PH 6.0; THEN SOAKED IN THE RESERVOIR SOLUTION PLUS 1 MM HAGPIA.
Crystal Properties
Matthews coefficientSolvent content
3.160

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.349α = 90
b = 65.349β = 90
c = 102.493γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC CCDSAGITALLY FOCUSING GE(220) AND A MULTILAYER2004-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
12.632.6299.60.16.25.414896
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)
12.62.7499.80.591.35.4

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 1AWR2.6301423075699.70.2130.2120.229RANDOM61.82
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]
5.212.65.21-7.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.826
r_scangle_it3.268
r_scbond_it1.779
r_angle_refined_deg1.404
r_mcangle_it1.377
r_angle_other_deg1.011
r_mcbond_it0.71
r_symmetry_vdw_other0.395
r_symmetry_vdw_refined0.265
r_nbd_other0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.826
r_scangle_it3.268
r_scbond_it1.779
r_angle_refined_deg1.404
r_mcangle_it1.377
r_angle_other_deg1.011
r_mcbond_it0.71
r_symmetry_vdw_other0.395
r_symmetry_vdw_refined0.265
r_nbd_other0.25
r_symmetry_hbond_refined0.219
r_nbd_refined0.185
r_xyhbond_nbd_refined0.145
r_nbtor_other0.087
r_chiral_restr0.082
r_bond_refined_d0.012
r_gen_planes_other0.012
r_gen_planes_refined0.008
r_bond_other_d0.004
r_dihedral_angle_4_deg
r_xyhbond_nbd_other
r_nbtor_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_metal_ion_refined
r_mcbond_other
r_metal_ion_other
r_mcangle_other
r_dihedral_angle_3_deg
r_scbond_other
r_dihedral_angle_2_deg
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 Atoms2562
Nucleic Acid Atoms
Solvent Atoms13
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing