4DL1

Crystal Structure of human Myeloperoxidase with covalent thioxanthine analog


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.529827% PEG 3350, 0.25 M CaCl2, betaine HCl, pH 5.5, vapor diffusion, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2545.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.829α = 90
b = 242.636β = 91.19
c = 151.505γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXEL ARRAY DETECTORPILATUS 6M2010-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.000APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.9242.63693.30.0917.13.1335809335809
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)
11.9267.40.4930.4931.61.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2128.492863251517397.60.193270.190450.24617RANDOM8.802
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]
-0.210.33-0.520.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.397
r_dihedral_angle_4_deg17.502
r_dihedral_angle_3_deg15.882
r_dihedral_angle_1_deg7.95
r_scangle_it4.238
r_scbond_it3.082
r_mcangle_it1.799
r_mcbond_it1.189
r_angle_refined_deg1.172
r_angle_other_deg0.734
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.397
r_dihedral_angle_4_deg17.502
r_dihedral_angle_3_deg15.882
r_dihedral_angle_1_deg7.95
r_scangle_it4.238
r_scbond_it3.082
r_mcangle_it1.799
r_mcbond_it1.189
r_angle_refined_deg1.172
r_angle_other_deg0.734
r_mcbond_other0.396
r_chiral_restr0.176
r_gen_planes_refined0.013
r_bond_refined_d0.01
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 Atoms36531
Nucleic Acid Atoms
Solvent Atoms2520
Heterogen Atoms1335

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling