☰ Navigation Tabs
Structure of McyB-C1A1 complexed with L-Leu and AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZXH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 3M sodium formate
Crystal Properties Matthews coefficient Solvent content 4.15 70.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.534 α = 90 b = 152.534 β = 90 c = 135.738 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 200K 2022-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 2.7 13.15 99.1 0.111 17.5 8 49972
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 2.7 2.79 1.274
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 2.7 13.15 47370 2540 98.93 0.21565 0.21274 0.2214 0.26941 0.2704 RANDOM 67.376
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] -0.04 -0.02 -0.04 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.922 r_long_range_B_refined 17.665 r_long_range_B_other 17.664 r_scangle_other 12.755 r_mcangle_it 12.069 r_mcangle_other 12.067 r_dihedral_angle_2_deg 9.375 r_dihedral_angle_1_deg 8.371 r_scbond_it 8.248 r_scbond_other 8.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.922 r_long_range_B_refined 17.665 r_long_range_B_other 17.664 r_scangle_other 12.755 r_mcangle_it 12.069 r_mcangle_other 12.067 r_dihedral_angle_2_deg 9.375 r_dihedral_angle_1_deg 8.371 r_scbond_it 8.248 r_scbond_other 8.247 r_mcbond_it 7.843 r_mcbond_other 7.843 r_angle_refined_deg 1.701 r_angle_other_deg 0.572 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 7301 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction BLU-MAX data collection Aimless data scaling