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Repeat domain 1 of Clostridium perfringens CPE0147
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MKM PDB ENTRY 4MKM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 10% PEG 20,000, 20% PEG MME 550, 0.02 M amino acids (0.02 M sodium L-glutamate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine, 0.02 M DL-serine), 0.1 M MOPS/HEPES ph 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.87 34.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.864 α = 90 b = 28.978 β = 115.6 c = 49.313 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 ADSC QUANTUM 315r 2013-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.72930 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.1 19.42 97.7 21.6 14.9 49641 49641
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 1.1 1.16 95.9 14.8 7065
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 4MKM 1.1 19.42 47054 47054 2571 97.39 0.18353 0.18353 0.18197 0.1738 0.21136 0.2051 RANDOM 17.93
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] 0.81 1.12 0.18 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.668 r_sphericity_free 29.342 r_sphericity_bonded 20.838 r_dihedral_angle_3_deg 12.382 r_rigid_bond_restr 11.453 r_dihedral_angle_1_deg 6.669 r_angle_refined_deg 1.348 r_chiral_restr 0.108 r_gen_planes_refined 0.019 r_bond_refined_d 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.668 r_sphericity_free 29.342 r_sphericity_bonded 20.838 r_dihedral_angle_3_deg 12.382 r_rigid_bond_restr 11.453 r_dihedral_angle_1_deg 6.669 r_angle_refined_deg 1.348 r_chiral_restr 0.108 r_gen_planes_refined 0.019 r_bond_refined_d 0.012 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1048 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling