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Wilavidin apo form (P1 form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7OUQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.6 M sodium citrate tribasic pH 6.5
Crystal Properties Matthews coefficient Solvent content 1.78 30.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.32 α = 103.53 b = 56.721 β = 110.75 c = 62.641 γ = 105.63
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 2M 2020-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96546 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.95 46.7 94.6 0.112 0.91 5.6 1.7 40032
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 1.95 2 0.674
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 7OUQ 1.95 46.7 38031 1971 94.58 0.1823 0.1801 0.1904 0.2259 0.2328 RANDOM 17.677
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] 1.08 -0.52 -0.28 -0.04 -0.44 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.189 r_dihedral_angle_3_deg 14.545 r_dihedral_angle_1_deg 8.332 r_dihedral_angle_4_deg 7.566 r_angle_refined_deg 1.721 r_angle_other_deg 1.352 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.189 r_dihedral_angle_3_deg 14.545 r_dihedral_angle_1_deg 8.332 r_dihedral_angle_4_deg 7.566 r_angle_refined_deg 1.721 r_angle_other_deg 1.352 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5481 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction autoPROC data reduction PHASER phasing