3ISQ

Crystal structure of human 4-Hydroxyphenylpyruvate dioxygenase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SQIPDB ENTRY 1SQI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52770.2M SODIUM ACETATE, 0.1M BIS-TRIS PROPANE PH 6.5, 20% PEG 3350, 10% ETHYLENE GLYCOL, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7755.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.206α = 90
b = 99.206β = 90
c = 87.726γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002009-08-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9778DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.7561.381000.110.0668.43.7506425063022
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.8499.90.7760.4642.23.77291

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1SQI1.7549.64810248037257299.960.145110.143620.17385RANDOM11.085
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]
0.320.160.32-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.502
r_dihedral_angle_4_deg17.525
r_dihedral_angle_3_deg12.182
r_dihedral_angle_1_deg6.309
r_scangle_it4.454
r_scbond_it2.693
r_mcangle_it1.534
r_angle_refined_deg1.475
r_angle_other_deg0.889
r_mcbond_it0.848
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.502
r_dihedral_angle_4_deg17.525
r_dihedral_angle_3_deg12.182
r_dihedral_angle_1_deg6.309
r_scangle_it4.454
r_scbond_it2.693
r_mcangle_it1.534
r_angle_refined_deg1.475
r_angle_other_deg0.889
r_mcbond_it0.848
r_mcbond_other0.275
r_chiral_restr0.1
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3033
Nucleic Acid Atoms
Solvent Atoms480
Heterogen Atoms19

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling