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Sirohaem decarboxylase AhbA/B - an enzyme with structural homology to the Lrp/AsnC transcription factor family that is part of the alternative haem biosynthesis pathway.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CZD PDB ENTRY 4CZD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 0.1M SODIUM ACETATE PH5, 0.2M AMMONIUM ACETATE, 30% PEG 4000, 0.01M BACL2, pH 5.0
Crystal Properties Matthews coefficient Solvent content 2.08 40.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.3 α = 90 b = 78.6 β = 90 c = 150.3 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 MIRRORS 2014-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 1.97 44 99.2 0.08 13.38 5.3 46648 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 1.97 2.02 97 0.8 2.5 4.9
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 4CZD 1.97 45.23 44314 2333 99.21 0.2049 0.20215 0.2077 0.25732 0.2612 RANDOM 39.406
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] -0.4 0.83 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.777 r_dihedral_angle_3_deg 18.025 r_dihedral_angle_4_deg 16.836 r_dihedral_angle_1_deg 6.868 r_mcangle_it 4.243 r_scbond_it 3.412 r_mcbond_it 2.769 r_mcbond_other 2.768 r_angle_refined_deg 2.235 r_angle_other_deg 0.981
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.777 r_dihedral_angle_3_deg 18.025 r_dihedral_angle_4_deg 16.836 r_dihedral_angle_1_deg 6.868 r_mcangle_it 4.243 r_scbond_it 3.412 r_mcbond_it 2.769 r_mcbond_other 2.768 r_angle_refined_deg 2.235 r_angle_other_deg 0.981 r_chiral_restr 0.136 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_gen_planes_other 0.004 r_bond_other_d 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_mcangle_other r_scbond_other r_scangle_it 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 4681 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing