2IVD

Structure of protoporphyrinogen oxidase from Myxococcus xanthus with acifluorfen


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.1M TRIS/HCL PH 7.5, 1.5M AMMONIUM SULPHATE, 20% GLYCEROL, 1% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
3.6666.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 148.918α = 90
b = 148.918β = 90
c = 131.924γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.1SRSPX14.1

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
12.349.475.20.078.72.5554191
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)
12.32.3846.70.531

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 DIFFRACTIONOTHERTHROUGHOUT2.349.3955419174886.30.2350.2340.283RANDOM33.82
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]
0.020.02-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.041
r_dihedral_angle_4_deg20.545
r_dihedral_angle_3_deg18.733
r_dihedral_angle_1_deg6.564
r_scangle_it1.835
r_angle_refined_deg1.487
r_scbond_it1.103
r_mcangle_it0.918
r_mcbond_it0.519
r_nbtor_refined0.296
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.041
r_dihedral_angle_4_deg20.545
r_dihedral_angle_3_deg18.733
r_dihedral_angle_1_deg6.564
r_scangle_it1.835
r_angle_refined_deg1.487
r_scbond_it1.103
r_mcangle_it0.918
r_mcbond_it0.519
r_nbtor_refined0.296
r_symmetry_vdw_refined0.258
r_nbd_refined0.193
r_symmetry_hbond_refined0.193
r_xyhbond_nbd_refined0.153
r_chiral_restr0.128
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6632
Nucleic Acid Atoms
Solvent Atoms288
Heterogen Atoms209

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling