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Crystal Structure of CMD1 in complex with vitamin C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7CY4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 5.6 290 2% Tacsimate, 0.1M CIT pH 5.6, 16% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.08 60.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.846 α = 90 b = 126.418 β = 102.27 c = 64.217 γ = 90
Symmetry Space Group C 1 2 1
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 PILATUS3 S 6M 2019-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9785 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 48.38 95.5 0.084 1 16.3 4.9 55672
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.25 97.6 1.03 0.65 1.8 5.1
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 THROUGHOUT 7CY4 2.2 48.38 53479 2000 91.34 0.1825 0.1811 0.1811 0.2209 0.2206 RANDOM 38.512
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] 1.21 0.06 -2.74 1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.09 r_sphericity_free 30.118 r_dihedral_angle_4_deg 19.555 r_sphericity_bonded 17.953 r_dihedral_angle_3_deg 15.9 r_dihedral_angle_1_deg 5.499 r_rigid_bond_restr 4.795 r_angle_refined_deg 1.291 r_chiral_restr 0.085 r_bond_refined_d 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.09 r_sphericity_free 30.118 r_dihedral_angle_4_deg 19.555 r_sphericity_bonded 17.953 r_dihedral_angle_3_deg 15.9 r_dihedral_angle_1_deg 5.499 r_rigid_bond_restr 4.795 r_angle_refined_deg 1.291 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6563 Nucleic Acid Atoms Solvent Atoms 402 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHENIX phasing