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Structure of the wild-type C3bot1 Exoenzyme (Nicotinamide-bound state, crystal form I)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GZF PDB ENTRY 1GZF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 22.5% PEG 3350 W/W, 100 MM LI2SO4, 100 MM SODIUM CITRATE PH 3.0, 3-10% MPEG 550 V/V
Crystal Properties Matthews coefficient Solvent content 2.26 45.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.741 α = 90 b = 74.638 β = 101.04 c = 118.962 γ = 90
Symmetry Space Group C 1 2 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 ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
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 1.69 24.32 99.5 0.04 25.6 4 99953 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1GZF 1.7 24.33 94351 4950 100 0.207 0.205 0.2121 0.235 0.2389 RANDOM 25.96
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] -0.84 -0.43 2.1 -1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.071 r_scangle_it 2.365 r_scbond_it 1.371 r_mcangle_it 1.025 r_angle_refined_deg 0.946 r_angle_other_deg 0.699 r_mcbond_it 0.531 r_nbd_other 0.231 r_nbd_refined 0.184 r_symmetry_vdw_other 0.173
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.071 r_scangle_it 2.365 r_scbond_it 1.371 r_mcangle_it 1.025 r_angle_refined_deg 0.946 r_angle_other_deg 0.699 r_mcbond_it 0.531 r_nbd_other 0.231 r_nbd_refined 0.184 r_symmetry_vdw_other 0.173 r_xyhbond_nbd_refined 0.131 r_symmetry_vdw_refined 0.121 r_symmetry_hbond_refined 0.116 r_nbtor_other 0.08 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6430 Nucleic Acid Atoms Solvent Atoms 782 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing