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Crystal structure of L-isoaspartyl protein carboxyl methyltranferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JG4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Oil batch 4.5 298 0.1M Acetate, 40% 1,2-propanediol, pH 4.5, Oil batch, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 3.29 62.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.267 α = 90 b = 84.448 β = 90 c = 123.091 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 120 CCD RIGAKU JUPITER 210 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0 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 50 98.1 0.037 6.9 43589 42769 -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 2 2.07 84.5 0.24 4.9 3629
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1JG4 2 20 40384 2143 98.52 0.1938 0.19182 0.23143 RANDOM 49.241
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] 2.94 1.48 -4.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.748 r_dihedral_angle_4_deg 16.581 r_dihedral_angle_3_deg 15.048 r_dihedral_angle_1_deg 6.464 r_scangle_it 4.785 r_scbond_it 3.078 r_mcangle_it 1.801 r_angle_refined_deg 1.8 r_mcbond_it 1.202 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.748 r_dihedral_angle_4_deg 16.581 r_dihedral_angle_3_deg 15.048 r_dihedral_angle_1_deg 6.464 r_scangle_it 4.785 r_scbond_it 3.078 r_mcangle_it 1.801 r_angle_refined_deg 1.8 r_mcbond_it 1.202 r_nbtor_refined 0.314 r_symmetry_hbond_refined 0.268 r_symmetry_vdw_refined 0.266 r_nbd_refined 0.224 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.121 r_bond_refined_d 0.02 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3308 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing