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Crystal Structure of Bacillus megaterium porphobilinogen deaminase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PDA PDB ENTRY 1PDA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.1M sodium cacodylate, 0.2M magnesium acetate, 25-30% PEG 8K, pH 6.5 - 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.47 50.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.32 α = 90 b = 65.78 β = 90 c = 97.21 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL PSI PILATUS 6M 2013-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
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 1.455 48.6 100 0.061 14.4 6.2 60772 60772
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 1.455 1.53 100 0.559 3 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1PDA 1.455 46.75 60772 57626 3073 99.98 0.14331 0.14112 0.139 0.18559 0.1842 RANDOM 23.972
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.127 r_sphericity_free 25.619 r_dihedral_angle_4_deg 22.985 r_dihedral_angle_3_deg 13.854 r_sphericity_bonded 11.816 r_rigid_bond_restr 8.154 r_dihedral_angle_1_deg 6.369 r_scbond_other 5.689 r_scbond_it 5.685 r_scangle_other 5.589
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.127 r_sphericity_free 25.619 r_dihedral_angle_4_deg 22.985 r_dihedral_angle_3_deg 13.854 r_sphericity_bonded 11.816 r_rigid_bond_restr 8.154 r_dihedral_angle_1_deg 6.369 r_scbond_other 5.689 r_scbond_it 5.685 r_scangle_other 5.589 r_long_range_B_refined 4.98 r_long_range_B_other 4.808 r_mcangle_other 3.331 r_mcangle_it 3.325 r_mcbond_it 2.796 r_mcbond_other 2.734 r_angle_refined_deg 2.438 r_angle_other_deg 2.208 r_chiral_restr 0.158 r_bond_refined_d 0.024 r_gen_planes_refined 0.012 r_bond_other_d 0.005 r_gen_planes_other 0.001 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2253 Nucleic Acid Atoms Solvent Atoms 325 Heterogen Atoms 65
Software Software Software Name Purpose GDA data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling