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Intermediate analogue in benzoylformate decarboxylase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MCZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.1 291 25% PEG 2000 w/v, 0.2M MgCl2 , pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.32 46.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.51 α = 63.46 b = 93.344 β = 72.82 c = 94.525 γ = 73.21
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 MAR CCD 165 mm 2007-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05 MPG/DESY, HAMBURG BW6
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 20 93.2 0.107 1.83 260986 243335 2 2 21.5
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) 1.62 1.64 92.3 0.39 2.1 1.82 9621
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 (All) 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 1MCZ 1.62 19.96 260986 230330 12259 92.95 0.17167 0.17167 0.17 0.1781 0.20309 0.2108 RANDOM 14.416
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] -0.19 -0.25 -0.37 0.32 -0.42 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.651 r_dihedral_angle_4_deg 13.563 r_dihedral_angle_3_deg 11.805 r_scangle_it 6.65 r_dihedral_angle_1_deg 5.917 r_scbond_it 4.947 r_mcangle_it 3.343 r_mcbond_it 2.942 r_angle_refined_deg 1.481 r_angle_other_deg 1.187
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.651 r_dihedral_angle_4_deg 13.563 r_dihedral_angle_3_deg 11.805 r_scangle_it 6.65 r_dihedral_angle_1_deg 5.917 r_scbond_it 4.947 r_mcangle_it 3.343 r_mcbond_it 2.942 r_angle_refined_deg 1.481 r_angle_other_deg 1.187 r_mcbond_other 0.913 r_symmetry_hbond_refined 0.233 r_symmetry_vdw_refined 0.222 r_nbd_refined 0.217 r_symmetry_vdw_other 0.216 r_nbd_other 0.185 r_xyhbond_nbd_refined 0.179 r_nbtor_refined 0.165 r_chiral_restr 0.106 r_nbtor_other 0.082 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16070 Nucleic Acid Atoms Solvent Atoms 2251 Heterogen Atoms 186
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling