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Crystal structure of the methylmalonyl-CoA mutase alpha-subunit from Aeropyrum pernix
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 oil batch 293 0.4M Ammonium dihydrogen phosphate, oil batch, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.662207 26.00201
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.902 α = 90 b = 51.134 β = 90 c = 54.564 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 CCD RIGAKU JUPITER 210 mirrors 2006-10-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 0.97884, 0.90000, 0.97938 SPring-8 BL26B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.8 50 99.8 0.067 17.8 6.6 11582 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 98.9 0.35 2.6
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 MAD THROUGHOUT 1.8 37.27 10970 552 99.56 0.21373 0.21194 0.2221 0.24713 0.2488 RANDOM 33.745
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] -0.79 0.52 0.27
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.835 r_dihedral_angle_1_deg 6.365 r_scbond_it 4.419 r_mcangle_it 2.888 r_angle_refined_deg 2.166 r_mcbond_it 1.633 r_angle_other_deg 1.002 r_nbd_other 0.255 r_symmetry_vdw_refined 0.252 r_nbd_refined 0.222
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.835 r_dihedral_angle_1_deg 6.365 r_scbond_it 4.419 r_mcangle_it 2.888 r_angle_refined_deg 2.166 r_mcbond_it 1.633 r_angle_other_deg 1.002 r_nbd_other 0.255 r_symmetry_vdw_refined 0.252 r_nbd_refined 0.222 r_symmetry_vdw_other 0.219 r_symmetry_hbond_refined 0.204 r_xyhbond_nbd_refined 0.2 r_chiral_restr 0.148 r_nbtor_other 0.092 r_bond_refined_d 0.033 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1074 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing