4YBN

Structure of the FAD and Heme binding protein msmeg_4975 from Mycobacterium smegmatis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FURPDB ID: 2FUR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP3.5291.1520% PEG1500, 4% MPD, 0.1 M citric acid
Crystal Properties
Matthews coefficientSolvent content
2.4850.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.722α = 90
b = 59.876β = 93.83
c = 89.658γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.9655Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.944.7399.60.1010.998137.535306
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9499.21.1090.762.17.62257

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 ID: 2FUR1.944.7333553174999.480.17630.17380.2228RANDOM33.33
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]
-1.88-0.152.21-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.833
r_dihedral_angle_4_deg16.254
r_dihedral_angle_3_deg14.652
r_dihedral_angle_1_deg6.869
r_mcangle_it3.85
r_mcbond_it2.78
r_mcbond_other2.776
r_angle_refined_deg1.896
r_angle_other_deg0.894
r_chiral_restr0.127
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.833
r_dihedral_angle_4_deg16.254
r_dihedral_angle_3_deg14.652
r_dihedral_angle_1_deg6.869
r_mcangle_it3.85
r_mcbond_it2.78
r_mcbond_other2.776
r_angle_refined_deg1.896
r_angle_other_deg0.894
r_chiral_restr0.127
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_gen_planes_other0.006
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3120
Nucleic Acid Atoms
Solvent Atoms326
Heterogen Atoms208

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement