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Crystal structure of VMB-1 at pH5.5(Bis-Tris)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6JV4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 289 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.29 46.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.11 α = 90 b = 97.11 β = 90 c = 132.66 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 2019-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97919 SSRF BL17U1
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 1.92 38.69 100 0.913 4.2 13.1 72855
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 1.97 0.793 2.1
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 6JV4 1.92 38.69 69071 3709 99.97 0.2023 0.2003 0.2093 0.2391 0.2395 RANDOM 31.774
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] -1.08 -0.7 1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.16 r_dihedral_angle_4_deg 17.279 r_dihedral_angle_3_deg 14.823 r_dihedral_angle_1_deg 7.01 r_angle_refined_deg 1.452 r_angle_other_deg 1.308 r_chiral_restr 0.068 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.16 r_dihedral_angle_4_deg 17.279 r_dihedral_angle_3_deg 14.823 r_dihedral_angle_1_deg 7.01 r_angle_refined_deg 1.452 r_angle_other_deg 1.308 r_chiral_restr 0.068 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6774 Nucleic Acid Atoms Solvent Atoms 409 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement xia2 data scaling PDB_EXTRACT data extraction xia2 data reduction PHASER phasing