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Anbu from Hyphomicrobium sp. strain MC1 -SG: R3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NYF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298.15 0.05 M ammonium sulfate, 0.05 M Bis-Tris, 30 % pentaerythritol propoxylate
Crystal Properties Matthews coefficient Solvent content 2.1 41.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 174.49 α = 90 b = 174.49 β = 90 c = 39.37 γ = 120
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 EIGER X 16M 2017-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 40 98.5 0.06 9.8 3.2 29744
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 2.1 99.7 0.532 2.5
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 5NYF 2 20 28233 1486 98.41 0.1836 0.18204 0.1885 0.21367 0.2192 RANDOM 59.642
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] -1.1 -0.55 -1.1 3.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.997 r_sphericity_free 31.143 r_dihedral_angle_4_deg 13.179 r_dihedral_angle_3_deg 12.081 r_sphericity_bonded 11.393 r_dihedral_angle_1_deg 5.439 r_long_range_B_refined 3.068 r_long_range_B_other 2.959 r_mcangle_it 2.284 r_mcangle_other 2.284
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.997 r_sphericity_free 31.143 r_dihedral_angle_4_deg 13.179 r_dihedral_angle_3_deg 12.081 r_sphericity_bonded 11.393 r_dihedral_angle_1_deg 5.439 r_long_range_B_refined 3.068 r_long_range_B_other 2.959 r_mcangle_it 2.284 r_mcangle_other 2.284 r_scangle_other 1.99 r_scbond_it 1.853 r_scbond_other 1.832 r_mcbond_it 1.813 r_mcbond_other 1.812 r_angle_refined_deg 0.995 r_angle_other_deg 0.819 r_rigid_bond_restr 0.734 r_chiral_restr 0.057 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3323 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing