4P2X

Swapped Dimer of Mycobacterial Adenylyl cyclase Rv1625c: Form 2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4P2MPDB ENTRY 4P2M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION8.52930.2M Lithium sulphate, Tris pH 8.5, 25% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
1.9235.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.57α = 90
b = 75.57β = 90
c = 133.17γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDbent collimating mirror and toroid2013-12-01SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.978565ESRFBM14

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
12.437.7899.80.0823.511.516832
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)
12.42.5399.60.5264.911.5

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 4P2M2.436.761598284999.750.199250.196230.25957RANDOM40.313
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]
-0.33-0.33-0.331.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.391
r_dihedral_angle_3_deg16.873
r_dihedral_angle_4_deg14.128
r_dihedral_angle_1_deg5.61
r_angle_refined_deg1.151
r_angle_other_deg0.705
r_chiral_restr0.066
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.391
r_dihedral_angle_3_deg16.873
r_dihedral_angle_4_deg14.128
r_dihedral_angle_1_deg5.61
r_angle_refined_deg1.151
r_angle_other_deg0.705
r_chiral_restr0.066
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms2535
Nucleic Acid Atoms
Solvent Atoms53
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
iMOSFLMdata reduction