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Crystal structure of hypothetical protein XCC2798 from Xanthomonas campestris, Target EFI-508608
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N1U pdb entry 3N1U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 273 85mM Tris-HCl, pH 8.5
0.17M sodium acetate
25.5% PEG4000,15% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.47 50.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.903 α = 90 b = 156.017 β = 90 c = 111.509 γ = 90
Symmetry Space Group C 2 2 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 CCD RAYONIX MX325HE 2013-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
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 2.69 111.51 99.4 0.083 17.2 7.1 21987 21866
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 2.69 2.83 100 0.426 4.2 7.5 3145
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 3N1U 2.69 78.01 20128 1095 96.61 0.24516 0.24358 0.2441 0.275 0.2767 RANDOM 49.199
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] -0.13 1.68 -1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.201 r_dihedral_angle_4_deg 18.113 r_dihedral_angle_3_deg 17.609 r_dihedral_angle_1_deg 5.449 r_long_range_B_refined 4.515 r_long_range_B_other 4.515 r_scangle_other 3.039 r_mcangle_it 2.447 r_mcangle_other 2.447 r_scbond_it 1.862
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.201 r_dihedral_angle_4_deg 18.113 r_dihedral_angle_3_deg 17.609 r_dihedral_angle_1_deg 5.449 r_long_range_B_refined 4.515 r_long_range_B_other 4.515 r_scangle_other 3.039 r_mcangle_it 2.447 r_mcangle_other 2.447 r_scbond_it 1.862 r_scbond_other 1.861 r_angle_refined_deg 1.524 r_mcbond_it 1.489 r_mcbond_other 1.489 r_angle_other_deg 1.196 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.006 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 5331 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing REFMAC refinement DENZO data reduction SCALA data scaling