3QHA

Crystal structure of a Putative oxidoreductase from Mycobacterium avium 104


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VPD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7289MyavA.01379.a.A1 22.39 mg/ml, 20% PEG 6000, 0.1 M Hepes pH 7.0, 0.2M CaCl2, cryo-protectant 25% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4149.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.055α = 90
b = 76.829β = 90
c = 115.879γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.97ALS5.0.1

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
12.25501000.1057.37.229158
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)
12.252.321000.6497.32415

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 REPLACEMENTTHROUGHOUT1VPD2.255028979147599.50.20130.19950.2338RANDOM28.4089
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]
0.53-1.220.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.036
r_dihedral_angle_4_deg14.598
r_dihedral_angle_3_deg13.206
r_dihedral_angle_1_deg5.34
r_scangle_it1.042
r_angle_refined_deg0.916
r_angle_other_deg0.841
r_scbond_it0.598
r_mcangle_it0.428
r_mcbond_it0.224
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.036
r_dihedral_angle_4_deg14.598
r_dihedral_angle_3_deg13.206
r_dihedral_angle_1_deg5.34
r_scangle_it1.042
r_angle_refined_deg0.916
r_angle_other_deg0.841
r_scbond_it0.598
r_mcangle_it0.428
r_mcbond_it0.224
r_chiral_restr0.053
r_mcbond_other0.026
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3968
Nucleic Acid Atoms
Solvent Atoms284
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction