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Anbu (Gly-1) mutant from Hyphomicrobium sp. strain MC1 - SG P2(1)2(1)2(1)
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 7 298.15 0.2 M Di-sodium tatrate, 20 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.86 56.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.25 α = 90 b = 116.3 β = 90 c = 197.84 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 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 2.4 40 98.5 0.079 14.1 5.3 92239
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 2.4 2.5 99.8 0.572 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 2.4 20 87461 4603 98.27 0.20614 0.20426 0.2084 0.24202 0.2456 RANDOM 45.954
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] -0.37 1.66 -1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.753 r_sphericity_free 29.965 r_dihedral_angle_4_deg 13.141 r_dihedral_angle_3_deg 12.982 r_dihedral_angle_1_deg 5.311 r_sphericity_bonded 3.958 r_long_range_B_refined 2.185 r_long_range_B_other 1.756 r_angle_refined_deg 0.99 r_mcangle_it 0.944
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.753 r_sphericity_free 29.965 r_dihedral_angle_4_deg 13.141 r_dihedral_angle_3_deg 12.982 r_dihedral_angle_1_deg 5.311 r_sphericity_bonded 3.958 r_long_range_B_refined 2.185 r_long_range_B_other 1.756 r_angle_refined_deg 0.99 r_mcangle_it 0.944 r_mcangle_other 0.944 r_scangle_other 0.855 r_rigid_bond_restr 0.823 r_angle_other_deg 0.813 r_mcbond_it 0.78 r_mcbond_other 0.78 r_scbond_it 0.668 r_scbond_other 0.668 r_chiral_restr 0.056 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 14678 Nucleic Acid Atoms Solvent Atoms 756 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing