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Crystal structure of circularly permuted CPDSBA_Q100T99: Preserved Global Fold and Local Structural Adjustments
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A2J PDB ENTRY 1A2J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 25% PEG 8000, 7-10% DMSO, 0.1M NA CACODYLATE PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.2 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.76 α = 90 b = 52.59 β = 103.23 c = 53.73 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 1999-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 2.4 20 99 0.056 17.4 7952
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 2.4 2.48 98.1 0.099 6.4
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 1A2J 2.4 20 7149 791 97.9 0.211 0.206 0.2051 0.256 0.2543 RANDOM 38.61
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] -1.92 3.87 -0.38 4.08
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.241 r_dihedral_angle_1_deg 3.566 r_scbond_it 2.982 r_mcangle_it 2.331 r_mcbond_it 1.14 r_angle_refined_deg 1.027 r_angle_other_deg 0.727 r_symmetry_vdw_other 0.292 r_nbd_other 0.257 r_symmetry_vdw_refined 0.243
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.241 r_dihedral_angle_1_deg 3.566 r_scbond_it 2.982 r_mcangle_it 2.331 r_mcbond_it 1.14 r_angle_refined_deg 1.027 r_angle_other_deg 0.727 r_symmetry_vdw_other 0.292 r_nbd_other 0.257 r_symmetry_vdw_refined 0.243 r_symmetry_hbond_refined 0.229 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.144 r_nbtor_other 0.086 r_chiral_restr 0.057 r_bond_refined_d 0.009 r_bond_other_d 0.005 r_gen_planes_refined 0.003 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 1447 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing