4X9M

Oxidized L-alpha-Glycerophosphate Oxidase from Mycoplasma pneumoniae with FAD bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DME 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5277.152.68 M NaCl, 2% v/v isopropanol, 0.1 M HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.7154.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.59α = 90
b = 111.59β = 90
c = 111.59γ = 90
Symmetry
Space GroupP 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.30.9765ALS5.0.3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.45010022.723.418401
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.53994.423.6

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 REPLACEMENTTHROUGHOUT3DME2.449.91744092399.770.150440.147620.20376RANDOM37.397
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_deg39.262
r_dihedral_angle_4_deg21.569
r_dihedral_angle_3_deg16.234
r_long_range_B_refined7.172
r_long_range_B_other7.111
r_dihedral_angle_1_deg6.853
r_scangle_other5.494
r_scbond_it3.673
r_scbond_other3.673
r_mcangle_it3.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.262
r_dihedral_angle_4_deg21.569
r_dihedral_angle_3_deg16.234
r_long_range_B_refined7.172
r_long_range_B_other7.111
r_dihedral_angle_1_deg6.853
r_scangle_other5.494
r_scbond_it3.673
r_scbond_other3.673
r_mcangle_it3.37
r_mcangle_other3.37
r_mcbond_it2.437
r_mcbond_other2.435
r_angle_refined_deg1.802
r_angle_other_deg0.986
r_chiral_restr0.114
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3000
Nucleic Acid Atoms
Solvent Atoms201
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
Cootmodel building
PHASERphasing