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Apo Crh5 transglycosylase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NDL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.1M sodium acetate trihydrate pH 4.0, 1,6M ammonium sulphate, 21mM ZnCl2
Crystal Properties Matthews coefficient Solvent content 2.26 45.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.4 α = 90 b = 74.171 β = 90 c = 116.82 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 PILATUS3 S 6M 2014-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.885601 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.25 62.62 99.01 0.807 7.99 4.1 23428
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.331 99.44 4.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5NDL 2.25 62.62 22150 1160 99.07 0.19404 0.19206 0.23101 0.2184 RANDOM 26.229
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] -1.51 0.49 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.364 r_dihedral_angle_4_deg 17.212 r_dihedral_angle_3_deg 16.149 r_long_range_B_refined 8.485 r_long_range_B_other 8.464 r_dihedral_angle_1_deg 7.605 r_scangle_other 4.562 r_mcangle_it 3.864 r_mcangle_other 3.863 r_scbond_it 2.813
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.364 r_dihedral_angle_4_deg 17.212 r_dihedral_angle_3_deg 16.149 r_long_range_B_refined 8.485 r_long_range_B_other 8.464 r_dihedral_angle_1_deg 7.605 r_scangle_other 4.562 r_mcangle_it 3.864 r_mcangle_other 3.863 r_scbond_it 2.813 r_scbond_other 2.812 r_mcbond_it 2.313 r_mcbond_other 2.31 r_angle_refined_deg 1.616 r_angle_other_deg 1.401 r_chiral_restr 0.072 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3664 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing