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Structure of A. niger Fdc1 in complex with alpha-methyl cinnamic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZA4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.2 M potassium thiocyanate, Bis-Tris propane 6.5, 20 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.4 48.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.94 α = 90 b = 64.17 β = 90 c = 87.73 γ = 90
Symmetry Space Group P 21 21 2
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 2014-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9 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 1.1 87.7 98 0.035 11.2 4.2 203456
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.1 1.13 97.8 2.4 2.7
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 4ZA4 1.1 30.05 203456 10579 99.98 0.13261 0.1322 0.136 0.14048 0.1466 RANDOM 10.253
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] 1.04 -2.22 1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.751 r_dihedral_angle_4_deg 20.896 r_dihedral_angle_3_deg 12.126 r_scangle_it 6.784 r_dihedral_angle_1_deg 6.346 r_scbond_it 5.081 r_mcangle_it 3.259 r_rigid_bond_restr 2.805 r_angle_refined_deg 2.469 r_mcbond_it 2.441
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.751 r_dihedral_angle_4_deg 20.896 r_dihedral_angle_3_deg 12.126 r_scangle_it 6.784 r_dihedral_angle_1_deg 6.346 r_scbond_it 5.081 r_mcangle_it 3.259 r_rigid_bond_restr 2.805 r_angle_refined_deg 2.469 r_mcbond_it 2.441 r_mcbond_other 2.421 r_angle_other_deg 1.774 r_chiral_restr 0.198 r_bond_refined_d 0.028 r_gen_planes_refined 0.018 r_gen_planes_other 0.013 r_bond_other_d 0.002 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_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3844 Nucleic Acid Atoms Solvent Atoms 465 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing