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Crystal structure of dKeima570 at pH 4.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8YDO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 Na-acetate, magnesium acetate, PEG8000
Crystal Properties Matthews coefficient Solvent content 2.17 43.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.584 α = 90 b = 84.584 β = 90 c = 105.296 γ = 120
Symmetry Space Group P 31 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 PIXEL DECTRIS PILATUS 6M 2022-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 11C 0.9794 PAL/PLS 11C
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 2.1 50 100 0.995 24.52 7.5 26036
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 2.1 2.14 0.456
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.1 31.67 23927 2002 99.84 0.2124 0.20861 0.2151 0.25869 0.264 RANDOM 43.864
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.511 r_long_range_B_other 11.181 r_long_range_B_refined 11.176 r_scangle_other 8.284 r_dihedral_angle_2_deg 7.873 r_dihedral_angle_1_deg 7.288 r_scbond_it 5.617 r_scbond_other 5.615 r_mcangle_it 5.444 r_mcangle_other 5.443
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.511 r_long_range_B_other 11.181 r_long_range_B_refined 11.176 r_scangle_other 8.284 r_dihedral_angle_2_deg 7.873 r_dihedral_angle_1_deg 7.288 r_scbond_it 5.617 r_scbond_other 5.615 r_mcangle_it 5.444 r_mcangle_other 5.443 r_mcbond_it 4.229 r_mcbond_other 4.208 r_angle_refined_deg 1.841 r_angle_other_deg 0.601 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 3470 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction MOLREP phasing PDB_EXTRACT data extraction