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Crystal structure of a Probable thiol peroxidase from Elizabethkingia anophelis NUHP1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JE1 4je1A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 Anatrace Morpheus screen, well g8: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD: 20mM of each sodium formate, ammonium acetate, trisodium citrate, sodium potassium Ltartrate, sodium oxamate: 100mM MOPS/HEPES-Na pH 7.5: ElanA.00055.a.B1, PW38308, at 23mg/ml: cryo: direct: tray 294018 g8: puck xoe2-6.
Crystal Properties Matthews coefficient Solvent content 2.21 44.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.59 α = 90 b = 107.8 β = 90 c = 113.7 γ = 90
Symmetry Space Group P 21 21 21
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 MX-300 2017-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.65 48.7 99.7 0.07 0.078 0.998 14.18 4.84 19753 64.797
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.72 99.8 0.618 0.693 0.882 2.84 4.983
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT 4je1A 2.65 48.7 1.35 19723 2096 99.58 0.2171 0.2095 0.2127 0.2805 0.2823 80.7365
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 13.449 f_angle_d 0.733 f_chiral_restr 0.048 f_plane_restr 0.006 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4546 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MoRDa phasing PHENIX model building Coot model building