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Crystal structure of Cordyceps militaris IDCase D323N mutant in apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HK5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 sitting drop 8.5 289 25% polyethylene glycol 3350, 0.2 M MgCl2, 0.1 M Tris-HCl, pH 8.5, sitting drop, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.59 52.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.618 α = 90 b = 77.618 β = 90 c = 140.089 γ = 90
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 RAYONIX MX225HE 2012-12-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9792 SSRF BL17U
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 2.4 77.62 97.1 0.103 9.5 3.5 31075
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 2.4 2.49 98.4 0.656 3.5 3125
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 4HK5 2.41 50 31074 1580 97.01 0.1838 0.1807 0.1784 0.2399 0.2398 RANDOM 57.078
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] 0.72 0.72 -1.43
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 34.311 r_dihedral_angle_2_deg 33.137 r_sphericity_free 29.559 r_dihedral_angle_3_deg 13.886 r_dihedral_angle_4_deg 12.601 r_dihedral_angle_1_deg 4.222 r_rigid_bond_restr 1.123 r_angle_refined_deg 0.975 r_chiral_restr 0.063 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 34.311 r_dihedral_angle_2_deg 33.137 r_sphericity_free 29.559 r_dihedral_angle_3_deg 13.886 r_dihedral_angle_4_deg 12.601 r_dihedral_angle_1_deg 4.222 r_rigid_bond_restr 1.123 r_angle_refined_deg 0.975 r_chiral_restr 0.063 r_bond_refined_d 0.005 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5339 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 2
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing