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Anbu (Gly-1) mutant 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 7.5 298.15 0.8 M sodium phosphate, 0.8 M potassium phosphate, 0.1 M HEPES
Crystal Properties Matthews coefficient Solvent content 2.14 42.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 175.548 α = 90 b = 175.548 β = 90 c = 39.742 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 2015-12-19 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 1.95 40 99.8 0.041 31.5 10.3 17067
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 1.95 2.05 99.7 0.584 4.27
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 1.95 20 16196 853 99.73 0.1793 0.17745 0.188 0.21414 0.2155 RANDOM 43.418
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] 0.19 0.1 0.19 -0.63
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 32.539 r_dihedral_angle_2_deg 32.207 r_dihedral_angle_4_deg 14.759 r_dihedral_angle_3_deg 12.132 r_sphericity_bonded 6.999 r_dihedral_angle_1_deg 5.541 r_long_range_B_refined 3.3 r_long_range_B_other 3.148 r_mcangle_it 2.186 r_mcangle_other 2.185
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 32.539 r_dihedral_angle_2_deg 32.207 r_dihedral_angle_4_deg 14.759 r_dihedral_angle_3_deg 12.132 r_sphericity_bonded 6.999 r_dihedral_angle_1_deg 5.541 r_long_range_B_refined 3.3 r_long_range_B_other 3.148 r_mcangle_it 2.186 r_mcangle_other 2.185 r_scangle_other 2.178 r_scbond_it 1.822 r_scbond_other 1.759 r_mcbond_other 1.707 r_mcbond_it 1.706 r_rigid_bond_restr 1.183 r_angle_refined_deg 1.085 r_angle_other_deg 0.842 r_chiral_restr 0.067 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 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 1672 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing