☰ Navigation Tabs
Structure of bacillus halmapalus alpha-amylase without any substrate analogues
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GJP PDB ENTRY 2GJP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 303 10 mM MES-HEPES, boric acid buffer, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 303K
Crystal Properties Matthews coefficient Solvent content 2.16 43.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.55 α = 90 b = 59.04 β = 90 c = 209.8 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 MARMOSAIC 225 mm CCD 2005-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1 MAX II I911-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 20 89.9 27805
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.2 98.6
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 (All) 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 PDB ENTRY 2GJP 2.1 19.95 26413 26413 1391 100 0.20189 0.20189 0.19978 0.2002 0.24216 0.2419 RANDOM 13.611
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] 1.82 -0.93 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.083 r_dihedral_angle_4_deg 15.833 r_dihedral_angle_3_deg 13.796 r_dihedral_angle_1_deg 5.898 r_mcangle_it 1.139 r_angle_refined_deg 1.106 r_scangle_it 1.049 r_mcbond_it 0.695 r_scbond_it 0.694 r_symmetry_hbond_refined 0.364
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.083 r_dihedral_angle_4_deg 15.833 r_dihedral_angle_3_deg 13.796 r_dihedral_angle_1_deg 5.898 r_mcangle_it 1.139 r_angle_refined_deg 1.106 r_scangle_it 1.049 r_mcbond_it 0.695 r_scbond_it 0.694 r_symmetry_hbond_refined 0.364 r_nbtor_refined 0.329 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.22 r_symmetry_vdw_refined 0.195 r_metal_ion_refined 0.12 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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_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 3915 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement ADSC data collection XDS data scaling MOLREP phasing