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Crystal structure of recombinant human fumarase in complex with D-2-amino-3-phosphono-propionic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UPP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 100 mM Hepes pH 7.5, 1% v/v 2-methylpentanediol and 16% m/v PEG 10 K
Crystal Properties Matthews coefficient Solvent content 3.05 59.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 190.903 α = 90 b = 190.903 β = 90 c = 116.243 γ = 120
Symmetry Space Group P 65 2 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 DECTRIS PILATUS 2M 2020-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS SIRUS BEAMLINE MANACA 1.3236 LNLS SIRUS MANACA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.15 49.85 100 0.999 15 39.2 67921
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.2 100 0.458 1.1
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 FREE R-VALUE 5UPP 2.15 49.85 64478 3399 99.99 0.1869 0.1858 0.1932 0.2088 0.2168 5% 47.766
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] 0.04 0.02 0.04 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.486 r_dihedral_angle_4_deg 19.305 r_dihedral_angle_3_deg 12.981 r_dihedral_angle_1_deg 5.819 r_angle_refined_deg 1.266 r_angle_other_deg 1.174 r_chiral_restr 0.052 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.486 r_dihedral_angle_4_deg 19.305 r_dihedral_angle_3_deg 12.981 r_dihedral_angle_1_deg 5.819 r_angle_refined_deg 1.266 r_angle_other_deg 1.174 r_chiral_restr 0.052 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6824 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing