6GMC

1.2 A resolution structure of human hydroxyacid oxidase 1 bound with FMN and 4-carboxy-5-[(4-chlorophenyl)sulfanyl]-1,2,3-thiadiazole


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29820% PEG3350 -- 10% ethylene glycol -- 0.1M bis-tris-propane pH 7.5 -- 0.2M sodium acetate
Crystal Properties
Matthews coefficientSolvent content
2.3848.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.348α = 90
b = 97.348β = 90
c = 80.363γ = 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
11.268.83599.50.0760.0880.0428.94.2115996115996
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)
11.21.2699.50.6880.6880.7930.3861.14.1

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 REPLACEMENTTHROUGHOUT2NZL1.238.31110271572399.390.13520.13420.1548RANDOM16.823
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]
-0.22-0.220.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.866
r_sphericity_free21.469
r_dihedral_angle_4_deg13.736
r_dihedral_angle_3_deg11.812
r_sphericity_bonded11.217
r_dihedral_angle_1_deg6.665
r_angle_refined_deg1.376
r_angle_other_deg1.015
r_rigid_bond_restr0.975
r_chiral_restr0.064
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.866
r_sphericity_free21.469
r_dihedral_angle_4_deg13.736
r_dihedral_angle_3_deg11.812
r_sphericity_bonded11.217
r_dihedral_angle_1_deg6.665
r_angle_refined_deg1.376
r_angle_other_deg1.015
r_rigid_bond_restr0.975
r_chiral_restr0.064
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2764
Nucleic Acid Atoms
Solvent Atoms303
Heterogen Atoms63

Software

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