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Degenerate RVD RG forms a distinct loop conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GJP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 8-10% PEG3350 (w/v), 10% ethanol and 0.1M MES pH 6.7
Crystal Properties Matthews coefficient Solvent content 2.9 57.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.169 α = 90 b = 93.622 β = 102.8 c = 167.632 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 130 mm 2017-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9793 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 3.09 50 98.8 0.092 2 4.6 73997
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.09 3.18 0.092
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 4GJP 3.1 50 73997 2348 89.01 0.24442 0.24264 0.2383 0.27782 0.2715 RANDOM 68.589
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] 2 2 -1.58 -1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.098 r_dihedral_angle_4_deg 22.477 r_dihedral_angle_3_deg 18.776 r_dihedral_angle_1_deg 6.022 r_long_range_B_other 2.487 r_long_range_B_refined 2.486 r_angle_refined_deg 1.34 r_angle_other_deg 1.268 r_mcangle_it 1.149 r_mcangle_other 1.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.098 r_dihedral_angle_4_deg 22.477 r_dihedral_angle_3_deg 18.776 r_dihedral_angle_1_deg 6.022 r_long_range_B_other 2.487 r_long_range_B_refined 2.486 r_angle_refined_deg 1.34 r_angle_other_deg 1.268 r_mcangle_it 1.149 r_mcangle_other 1.148 r_scangle_other 0.909 r_mcbond_it 0.63 r_mcbond_other 0.628 r_scbond_it 0.494 r_scbond_other 0.494 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.005 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 14420 Nucleic Acid Atoms 2764 Solvent Atoms 10 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction SCALEPACK data scaling PHASER phasing