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Class II aldolase HpcH - magnesium - oxamate complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DXE PDB ENTRY 1DXE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 0.4 M AMMONIUM DIHYDROGEN PHOSPHATE, 30% (V/V) GLYCEROL, 0.01M MAGNESIUM CHLORIDE AND 0.01M SODIUM OXAMATE., pH 5
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.2 α = 90 b = 152.2 β = 90 c = 152.2 γ = 90
Symmetry Space Group P 21 3
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 ADSC CCD MIRRORS 2005-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 SRS PX14.2
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 2.2 50.8 99.8 0.07 20.5 6.3 59541 -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 2.2 2.23 99.8 0.53 2.5 5.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1DXE 2.2 50.77 57191 2350 99.8 0.171 0.171 0.1639 0.192 0.1844 RANDOM 30.77
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.182 r_dihedral_angle_3_deg 14.742 r_dihedral_angle_4_deg 13.594 r_dihedral_angle_1_deg 5.573 r_scangle_it 3.453 r_scbond_it 2.148 r_angle_refined_deg 1.377 r_mcangle_it 1.158 r_mcbond_it 0.692 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.182 r_dihedral_angle_3_deg 14.742 r_dihedral_angle_4_deg 13.594 r_dihedral_angle_1_deg 5.573 r_scangle_it 3.453 r_scbond_it 2.148 r_angle_refined_deg 1.377 r_mcangle_it 1.158 r_mcbond_it 0.692 r_nbtor_refined 0.297 r_symmetry_vdw_refined 0.21 r_nbd_refined 0.198 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.089 r_bond_refined_d 0.014 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3948 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing