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Porphobilinogen Deaminase from Arabidopsis Thaliana
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 5.6 293 5 mg/ml protein added in 50:50 ratio to the well-solution of 25% PEG 4000, 100 mM sodium citrate, 200 mM ammonium sulphate. Crystals grown in the dark due to photosensitivity of the cofactor., pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.02 39.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.573 α = 90 b = 37.271 β = 105 c = 55.069 γ = 90
Symmetry Space Group C 1 2 1
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 QUANTUM 315 2007-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.979 ESRF ID29
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 1.45 32.89 99.3 0.098 5.6 3.6 49235 15.1
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 1.45 1.53 99.4 0.767 2.2 3.5 7129
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1PDA 1.45 32.89 46662 2455 99.03 0.14859 0.14495 0.1424 0.21707 0.2159 RANDOM 22.927
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] 0.34 0.1 -0.55 0.26
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.308 r_dihedral_angle_2_deg 36.967 r_sphericity_bonded 19.639 r_dihedral_angle_4_deg 16.794 r_dihedral_angle_3_deg 15.465 r_rigid_bond_restr 6.36 r_dihedral_angle_1_deg 5.763 r_angle_refined_deg 2.052 r_chiral_restr 0.135 r_bond_refined_d 0.02
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.308 r_dihedral_angle_2_deg 36.967 r_sphericity_bonded 19.639 r_dihedral_angle_4_deg 16.794 r_dihedral_angle_3_deg 15.465 r_rigid_bond_restr 6.36 r_dihedral_angle_1_deg 5.763 r_angle_refined_deg 2.052 r_chiral_restr 0.135 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2289 Nucleic Acid Atoms Solvent Atoms 409 Heterogen Atoms 35
Software Software Software Name Purpose MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling