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Apo Class II aldolase HpcH
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, pH 5
Crystal Properties Matthews coefficient Solvent content 2.3 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.92 α = 90 b = 128.92 β = 90 c = 175.3 γ = 120
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 MARRESEARCH MIRRORS 2005-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 1.6 40.8 100 0.07 33.6 10.9 73671 -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 1.6 1.64 100 0.71 2.5 10.5
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 1.6 40.79 70689 2982 100 0.174 0.173 0.1724 0.207 0.2067 RANDOM 23.27
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] 0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.219 r_dihedral_angle_4_deg 14.419 r_dihedral_angle_3_deg 12.743 r_dihedral_angle_1_deg 5.217 r_scangle_it 3.991 r_scbond_it 2.495 r_mcangle_it 1.485 r_angle_refined_deg 1.471 r_mcbond_it 0.935 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.219 r_dihedral_angle_4_deg 14.419 r_dihedral_angle_3_deg 12.743 r_dihedral_angle_1_deg 5.217 r_scangle_it 3.991 r_scbond_it 2.495 r_mcangle_it 1.485 r_angle_refined_deg 1.471 r_mcbond_it 0.935 r_nbtor_refined 0.311 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.199 r_symmetry_hbond_refined 0.138 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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 4007 Nucleic Acid Atoms Solvent Atoms 511 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing