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Anbu from Hyphomicrobium sp. strain MC1 - SG: R32
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 8.5 298.15 0.1 M Tris, 2.0 M ammonium phosphate
Crystal Properties Matthews coefficient Solvent content 2.43 49.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 176.217 α = 90 b = 176.217 β = 90 c = 39.551 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 PILATUS 6M 2016-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0 ESRF ID23-1
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 1.9 40 99.6 0.045 17 4.2 18422
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 1.9 2 99.7 0.597 2.7
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 1.9 20 17483 921 99.46 0.1909 0.18961 0.1989 0.2152 0.2226 RANDOM 42.786
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] 0.26 0.13 0.26 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.509 r_sphericity_free 29.478 r_dihedral_angle_4_deg 13.836 r_dihedral_angle_3_deg 11.628 r_sphericity_bonded 5.393 r_dihedral_angle_1_deg 5.26 r_long_range_B_refined 2.259 r_long_range_B_other 2.12 r_mcangle_it 1.651 r_mcangle_other 1.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.509 r_sphericity_free 29.478 r_dihedral_angle_4_deg 13.836 r_dihedral_angle_3_deg 11.628 r_sphericity_bonded 5.393 r_dihedral_angle_1_deg 5.26 r_long_range_B_refined 2.259 r_long_range_B_other 2.12 r_mcangle_it 1.651 r_mcangle_other 1.65 r_mcbond_it 1.278 r_mcbond_other 1.278 r_scangle_other 1.271 r_scbond_it 1.06 r_scbond_other 1.044 r_angle_refined_deg 1.028 r_angle_other_deg 0.831 r_rigid_bond_restr 0.64 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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 1717 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing