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Structure of protoporphyrinogen oxidase from Myxococcus xanthus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SEZ PDB ENTRY 1SEZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1M TRIS/HCL PH 7.5, 1.5M AMMONIUM SULPHATE, 20% GLYCEROL, 1% PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.74 66.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.566 α = 90 b = 148.566 β = 90 c = 132.745 γ = 90
Symmetry Space Group P 4 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 SRS PX14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.7 74.3 100 0.14 14.7 7.5 41382 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.85 99.8 0.57 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1SEZ 2.7 74.33 40498 857 99.9 0.248 0.247 0.287 0.2543 RANDOM 30.6
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] -0.02 -0.02 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.385 r_dihedral_angle_3_deg 17.243 r_dihedral_angle_4_deg 16.514 r_dihedral_angle_1_deg 4.828 r_angle_refined_deg 1.122 r_scangle_it 0.764 r_mcangle_it 0.484 r_scbond_it 0.431 r_nbtor_refined 0.295 r_mcbond_it 0.269
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.385 r_dihedral_angle_3_deg 17.243 r_dihedral_angle_4_deg 16.514 r_dihedral_angle_1_deg 4.828 r_angle_refined_deg 1.122 r_scangle_it 0.764 r_mcangle_it 0.484 r_scbond_it 0.431 r_nbtor_refined 0.295 r_mcbond_it 0.269 r_nbd_refined 0.189 r_symmetry_vdw_refined 0.161 r_xyhbond_nbd_refined 0.118 r_symmetry_hbond_refined 0.114 r_chiral_restr 0.068 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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 Atoms Number Protein Atoms 6648 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 217
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing MOLREP phasing REFMAC refinement