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Crystal structure of Bacillus megaterium porphobilinogen deaminase
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 2.42 49.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.01 α = 90 b = 65.12 β = 90 c = 96.78 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 CCD MARMOSAIC 225 mm CCD 2013-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 1.072 ESRF BM14
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 1.6 31.33 95.6 0.088 10.1 6.4 42866 42866
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 1.6 1.69 88.7 1.493 0.9 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 1.6 31.33 42728 40552 2176 95.05 0.16462 0.16061 0.24215 0.2334 RANDOM 28.019
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] -0.16 0.47 -0.31
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.063 r_dihedral_angle_2_deg 35.539 r_dihedral_angle_4_deg 22.7 r_sphericity_bonded 19.976 r_dihedral_angle_3_deg 15.1 r_scangle_other 8.648 r_long_range_B_refined 8.563 r_long_range_B_other 8.56 r_scbond_it 7.874 r_scbond_other 7.871
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.063 r_dihedral_angle_2_deg 35.539 r_dihedral_angle_4_deg 22.7 r_sphericity_bonded 19.976 r_dihedral_angle_3_deg 15.1 r_scangle_other 8.648 r_long_range_B_refined 8.563 r_long_range_B_other 8.56 r_scbond_it 7.874 r_scbond_other 7.871 r_mcangle_other 6.968 r_mcangle_it 6.947 r_dihedral_angle_1_deg 6.18 r_mcbond_it 5.839 r_mcbond_other 5.828 r_rigid_bond_restr 5.224 r_angle_refined_deg 2.142 r_angle_other_deg 1.526 r_chiral_restr 0.121 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.004 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 2245 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 65
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling