1TKL

Yeast Oxygen-Dependent Coproporphyrinogen Oxidase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.527718% PEG 8000, 0.1 M HEPES, 2% isopropanol, 0.2 M sodium acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.350

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.822α = 90
b = 86.822β = 90
c = 207.835γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.10NSLSX25

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
123098.40.0570.0571995106434.1
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)
22.0797.50.5830.5833.29.15248

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONChromium sulfur SADTHROUGHOUT279.065106451064273298.390.21010.21010.207570.25828RANDOM34.09
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]
1.51.5-2.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34
r_dihedral_angle_4_deg19.944
r_dihedral_angle_3_deg16.043
r_dihedral_angle_1_deg7.29
r_scangle_it3.07
r_scbond_it2.242
r_mcangle_it1.696
r_mcbond_it1.508
r_angle_refined_deg1.507
r_angle_other_deg0.898
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34
r_dihedral_angle_4_deg19.944
r_dihedral_angle_3_deg16.043
r_dihedral_angle_1_deg7.29
r_scangle_it3.07
r_scbond_it2.242
r_mcangle_it1.696
r_mcbond_it1.508
r_angle_refined_deg1.507
r_angle_other_deg0.898
r_symmetry_vdw_other0.26
r_mcbond_other0.238
r_nbd_refined0.211
r_symmetry_vdw_refined0.203
r_nbd_other0.197
r_symmetry_hbond_refined0.187
r_nbtor_refined0.186
r_xyhbond_nbd_refined0.164
r_chiral_restr0.099
r_nbtor_other0.088
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5291
Nucleic Acid Atoms
Solvent Atoms418
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing