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Ni-Carbonic Anhydrase II complexed with 3NPA after UV at 200 K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LV5 6LV5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 293 1.3 M sodium citrate, 50 mM Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.09 41.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.49 α = 90 b = 41.324 β = 104.04 c = 71.965 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 200 CCD ADSC QUANTUM 270 2020-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
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 1.5 30 97 0.06 0.071 0.037 0.995 20.6 3.8 37959
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 1.5 1.53 94.6 0.438 0.509 0.259 0.829 4.1 3.8
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 FREE R-VALUE 6LV5 1.5 29.18 35950 1929 96.9 0.11316 0.1107 0.1107 0.15796 0.1589 RANDOM 21.333
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] -0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 55.299 r_dihedral_angle_2_deg 36.707 r_dihedral_angle_4_deg 24.503 r_sphericity_bonded 14.959 r_dihedral_angle_3_deg 14.306 r_long_range_B_refined 6.99 r_long_range_B_other 6.989 r_dihedral_angle_1_deg 6.63 r_scangle_other 5.738 r_rigid_bond_restr 4.982
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 55.299 r_dihedral_angle_2_deg 36.707 r_dihedral_angle_4_deg 24.503 r_sphericity_bonded 14.959 r_dihedral_angle_3_deg 14.306 r_long_range_B_refined 6.99 r_long_range_B_other 6.989 r_dihedral_angle_1_deg 6.63 r_scangle_other 5.738 r_rigid_bond_restr 4.982 r_scbond_it 4.971 r_scbond_other 4.93 r_mcangle_it 3.405 r_mcangle_other 3.403 r_mcbond_it 3.216 r_mcbond_other 3.023 r_angle_refined_deg 2.468 r_angle_other_deg 1.248 r_chiral_restr 0.185 r_bond_refined_d 0.029 r_gen_planes_refined 0.013 r_gen_planes_other 0.004 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2049 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing