☰ Navigation Tabs
Crystal structure of CcbD C19S mutant complexed with single PCP domain of CcbZ
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9DKR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 0.2 M sodium malonate, 20% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.55 51.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.28 α = 90 b = 89.079 β = 90 c = 135.029 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS3 S 6M 2022-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11588 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.55 135.03 100 0.076 0.083 0.032 1 18.7 13 132094
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 100 1.973 2.141 0.826 0.649 1.5 12.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.55 74.467 131999 6716 99.988 0.178 0.1769 0.1766 0.2051 0.2047 25.25
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] 2.254 -1.342 -0.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.87 r_dihedral_angle_4_deg 17.298 r_dihedral_angle_3_deg 12.714 r_lrange_it 6.062 r_dihedral_angle_1_deg 5.983 r_lrange_other 5.972 r_scangle_it 4.828 r_scangle_other 4.827 r_scbond_it 3.301 r_scbond_other 3.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.87 r_dihedral_angle_4_deg 17.298 r_dihedral_angle_3_deg 12.714 r_lrange_it 6.062 r_dihedral_angle_1_deg 5.983 r_lrange_other 5.972 r_scangle_it 4.828 r_scangle_other 4.827 r_scbond_it 3.301 r_scbond_other 3.301 r_mcangle_it 2.962 r_mcangle_other 2.962 r_mcbond_it 2.143 r_mcbond_other 2.143 r_angle_refined_deg 1.674 r_angle_other_deg 1.546 r_nbd_refined 0.215 r_nbd_other 0.192 r_symmetry_nbd_other 0.181 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.153 r_symmetry_xyhbond_nbd_refined 0.137 r_chiral_restr 0.091 r_symmetry_nbd_refined 0.085 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.053 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5949 Nucleic Acid Atoms Solvent Atoms 660 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing