2RDW

Crystal Structure of Human Glycolate Oxidase in Complex with Sulfate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GOXPDB ENTRY 1GOX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5298HEPES,PEG 600, Li2SO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.3463.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.649α = 90
b = 143.649β = 90
c = 110.461γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42006-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4A0.9793NSLSX4A

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
11.9528.1792.30.0518.94.83389113
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)
11.952.0286.60.2254.22.623597

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 ENTRY 1GOX1.9527.7738909197192.270.1990.1970.235RANDOM15.698
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]
-0.16-0.160.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.863
r_dihedral_angle_4_deg17.143
r_dihedral_angle_3_deg16.903
r_dihedral_angle_1_deg6.034
r_scangle_it3.025
r_scbond_it1.964
r_angle_refined_deg1.6
r_mcangle_it1.082
r_mcbond_it0.755
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.863
r_dihedral_angle_4_deg17.143
r_dihedral_angle_3_deg16.903
r_dihedral_angle_1_deg6.034
r_scangle_it3.025
r_scbond_it1.964
r_angle_refined_deg1.6
r_mcangle_it1.082
r_mcbond_it0.755
r_nbtor_refined0.305
r_nbd_refined0.205
r_symmetry_vdw_refined0.19
r_symmetry_hbond_refined0.183
r_xyhbond_nbd_refined0.149
r_chiral_restr0.13
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2794
Nucleic Acid Atoms
Solvent Atoms220
Heterogen Atoms36

Software

Software
Software NamePurpose
d*TREKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
d*TREKdata reduction