☰ Navigation Tabs
Crystal Structure of Methylitaconate-delta-isomerase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PW0 PDB ENTRY 2PW0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 Protein solution: 150mM Tris/HCl, 150mM NaCl; Reservoir solution: 23% PEG 1500, 18% glycerol anhydrous.
0.001ml protein plus 0.001ml reservoir, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.59 52.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.078 α = 90 b = 142.077 β = 90 c = 228.452 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 MARMOSAIC 225 mm CCD LN2 cooled fixed-exit, Si(111) monochromator; Dynamically bendable mirror 2008-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0707 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.7 50 98 0.086 0.086 20.6 4 47521
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.7 2.8 95.4 0.434 0.434 2.6 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2PW0 2.7 50 63650 45050 2402 97.78 0.20267 0.19986 0.25559 0.2341 RANDOM 46.36
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] 1.42 1.69 -3.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.322 r_dihedral_angle_4_deg 24.971 r_dihedral_angle_3_deg 19.102 r_dihedral_angle_1_deg 7.497 r_scangle_it 2.683 r_scbond_it 1.619 r_angle_refined_deg 1.485 r_mcangle_it 1.182 r_mcbond_it 0.704 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.322 r_dihedral_angle_4_deg 24.971 r_dihedral_angle_3_deg 19.102 r_dihedral_angle_1_deg 7.497 r_scangle_it 2.683 r_scbond_it 1.619 r_angle_refined_deg 1.485 r_mcangle_it 1.182 r_mcbond_it 0.704 r_nbtor_refined 0.31 r_symmetry_hbond_refined 0.243 r_nbd_refined 0.223 r_symmetry_vdw_refined 0.214 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 10127 Nucleic Acid Atoms Solvent Atoms 465 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling