3OI9

Crystal structure of molybdenum cofactor synthesis domain from Mycobacterium avium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2G4R2g4r molecule a

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP528929.9 mg/mL MyavA.00778.b.A1 PW28925 against EBS PACT screen condition A8, 0.2 M ammonium chloride, 0.1 M sodium acetate pH 5.0, 20% PEG 6000 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 217062a8, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.1342.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.03α = 90
b = 68.03β = 90
c = 53.17γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2010-08-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

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
11.955099.60.04619.073.91031410275-333.744
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)
11.95299.60.4412

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 REPLACEMENTTHROUGHOUT2g4r molecule a1.95501025449399.430.19870.19620.2446RANDOM40.3835
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.193
r_dihedral_angle_4_deg11.838
r_dihedral_angle_3_deg11.531
r_dihedral_angle_1_deg4.62
r_scangle_it3.445
r_scbond_it1.985
r_angle_refined_deg1.361
r_mcangle_it1.262
r_mcbond_it0.713
r_chiral_restr0.088
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.193
r_dihedral_angle_4_deg11.838
r_dihedral_angle_3_deg11.531
r_dihedral_angle_1_deg4.62
r_scangle_it3.445
r_scbond_it1.985
r_angle_refined_deg1.361
r_mcangle_it1.262
r_mcbond_it0.713
r_chiral_restr0.088
r_bond_refined_d0.014
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1032
Nucleic Acid Atoms
Solvent Atoms79
Heterogen Atoms

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
XDSdata reduction