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Crystal structure of a cysteine hydrolase from Ustilago maydis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8RKZ Crystal structure of a homolog from Phytophthora infestans
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Tris pH 7.0, 20% PEG-2000
Crystal Properties Matthews coefficient Solvent content 1.83 32.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.25 α = 90 b = 94.25 β = 90 c = 40.03 γ = 90
Symmetry Space Group P 4 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 DECTRIS PILATUS 6M 2020-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.976253 ESRF MASSIF-3
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 1.81 42.15 99.71 0.1354 0.997 10.4 11.9 16972 33.31
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 1.81 1.875 2.842 0.695 0.96
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.81 42.15 1.35 16971 848 99.41 0.2192 0.2172 0.217 0.2579 0.2579 46.16
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.032 f_angle_d 0.8424 f_chiral_restr 0.0534 f_bond_d 0.0062 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1570 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing