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Crystal structure of Prc with PDZ domain deletion in complex with NlpI
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WQL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 PEG3350, sodium citrate tribasic dihydrate
Crystal Properties Matthews coefficient Solvent content 2.97 58.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.827 α = 90 b = 151.082 β = 90 c = 148.38 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 110 CCD RAYONIX MX300HE LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator , A Pair of K-B Focusing Mirrors 2018-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 0.99984 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.9 50 95.9 0.057 0.088 0.042 18.95 4.4 25531
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 2.9 3 76 0.201 0.276 0.141 0.963 4.39 3.4
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 5WQL 2.9 38.8 22490 1192 88.88 0.19398 0.1919 0.1948 0.2334 0.2412 RANDOM 49.792
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.855 r_dihedral_angle_4_deg 20.457 r_dihedral_angle_3_deg 19.522 r_long_range_B_refined 10.693 r_long_range_B_other 10.692 r_dihedral_angle_1_deg 7.186 r_scangle_other 7.118 r_mcangle_it 7.082 r_mcangle_other 7.081 r_scbond_it 4.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.855 r_dihedral_angle_4_deg 20.457 r_dihedral_angle_3_deg 19.522 r_long_range_B_refined 10.693 r_long_range_B_other 10.692 r_dihedral_angle_1_deg 7.186 r_scangle_other 7.118 r_mcangle_it 7.082 r_mcangle_other 7.081 r_scbond_it 4.78 r_scbond_other 4.769 r_mcbond_it 4.734 r_mcbond_other 4.732 r_angle_refined_deg 1.765 r_angle_other_deg 1.278 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 6434 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing Coot model building HKL-2000 data reduction