2XWM

Crystal structure of IspD from Mycobacterium smegmatis in complex with CMP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293SITTING-DROP VAPOR-DIFFUSION METHOD AT 293 K. DROPS WITH 300 NANOLITERS PROTEIN SOLUTION (PROTEIN AT 40 MG/ML IN 20 MM BIS-TRIS-PROPANE, PH 6.5, 0.1 M NACL WITH 10 MM CMP, 10 MM MGCL2 AND 10 MM ERYTHRITOL) AND 300 NANOLITERS SCREENING/RESERVOIR SOLUTION (10% (W/V) PEG 20,000, 20% (V/V) MONOMETHYL ETHER PEG 550, 0.03M NAF, 0.03M NAI, 0.03M NABR, AND 0.1M MOPS/NA-HEPES, PH 7.5)
Crystal Properties
Matthews coefficientSolvent content
2.0439.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.59α = 90
b = 71.7β = 90
c = 111.89γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 4r2010-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.82899.90.0916.2734794
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)
11.81.999.90.563.57

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.860.3732984175099.880.181850.180070.21529RANDOM23.465
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]
1.03-0.86-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.107
r_dihedral_angle_4_deg16.821
r_dihedral_angle_3_deg12.99
r_dihedral_angle_1_deg5.365
r_angle_refined_deg1.254
r_chiral_restr0.073
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.107
r_dihedral_angle_4_deg16.821
r_dihedral_angle_3_deg12.99
r_dihedral_angle_1_deg5.365
r_angle_refined_deg1.254
r_chiral_restr0.073
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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 Atoms3156
Nucleic Acid Atoms
Solvent Atoms274
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing