☰ Navigation Tabs
Crystal Structure of Cobalamin biosynthesis precorrin 8W decarboxylase (cbiT)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 OIL BATCH 6 298 50% PEG 400, 0.1M MES, pH 6.0, OIL BATCH, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.13 42.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.442 α = 90 b = 93.442 β = 90 c = 81.042 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD RIGAKU JUPITER 210 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 0.97891, 0.90000, 0.97928 SPring-8 BL26B1
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 2.3 50 98.9 0.089 12.6 16507 16322 -3
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 2.3 2.38 94.4 0.36 9.6 1539
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.3 20 14721 788 94.23 0.20171 0.19793 0.27322 RANDOM 49.032
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] 1.8 1.8 -3.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.42 r_dihedral_angle_3_deg 18.858 r_dihedral_angle_4_deg 15.103 r_dihedral_angle_1_deg 7.252 r_scangle_it 6.376 r_scbond_it 4.139 r_angle_refined_deg 2.486 r_mcangle_it 2.455 r_mcbond_it 1.553 r_nbtor_refined 0.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.42 r_dihedral_angle_3_deg 18.858 r_dihedral_angle_4_deg 15.103 r_dihedral_angle_1_deg 7.252 r_scangle_it 6.376 r_scbond_it 4.139 r_angle_refined_deg 2.486 r_mcangle_it 2.455 r_mcbond_it 1.553 r_nbtor_refined 0.333 r_symmetry_vdw_refined 0.32 r_nbd_refined 0.27 r_chiral_restr 0.195 r_xyhbond_nbd_refined 0.193 r_symmetry_hbond_refined 0.175 r_bond_refined_d 0.031 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2763 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction SCALEPACK data scaling SOLVE phasing