6GMB

Structure of human hydroxyacid oxidase 1 bound with FMN and glycolate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NZL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29030% PEG1000 -- 0.1M MIB pH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.3748.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.431α = 90
b = 97.431β = 90
c = 80.364γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2018-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.3568.89499.20.040.0430.01729.26.28152181521
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.4294.90.0930.0930.1070.0527.23.9

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 REPLACEMENTTHROUGHOUT2NZL1.3540.2177545397699.160.1110.110.1302RANDOM14.354
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]
-0.32-0.320.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.515
r_sphericity_free22.899
r_dihedral_angle_4_deg13.054
r_dihedral_angle_3_deg11.103
r_sphericity_bonded8.307
r_dihedral_angle_1_deg6.228
r_angle_refined_deg1.258
r_angle_other_deg0.987
r_rigid_bond_restr0.743
r_chiral_restr0.063
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.515
r_sphericity_free22.899
r_dihedral_angle_4_deg13.054
r_dihedral_angle_3_deg11.103
r_sphericity_bonded8.307
r_dihedral_angle_1_deg6.228
r_angle_refined_deg1.258
r_angle_other_deg0.987
r_rigid_bond_restr0.743
r_chiral_restr0.063
r_gen_planes_refined0.006
r_bond_refined_d0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2791
Nucleic Acid Atoms
Solvent Atoms376
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
SCALAdata scaling
PHASERphasing
XDSdata reduction