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Glycoside Hydrolase Family 15 Glucoamylase from Hypocrea jecorina
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VN4 PDB ENTRY 2VN4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 25% PEG3350, 0.10M CACL2, 0.10M BIS-TRIS PH 5.5
Crystal Properties Matthews coefficient Solvent content 2.07 40.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 216.756 α = 90 b = 48.49 β = 90.49 c = 50.562 γ = 90
Symmetry Space Group C 1 2 1
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 2007-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-5 MAX II I911-5
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 1.9 16.98 99.8 0.08 19.7 5.4 41660 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 1.9 2 99.5 0.4 3 4.9
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 PDB ENTRY 2VN4 1.9 16.96 39555 2102 99.88 0.20365 0.20109 0.25331 RANDOM 24.022
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] -1.83 -0.16 2.86 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.759 r_dihedral_angle_4_deg 14.785 r_dihedral_angle_3_deg 12.833 r_dihedral_angle_1_deg 5.574 r_scangle_it 1.896 r_scbond_it 1.394 r_angle_refined_deg 1.218 r_mcangle_it 0.866 r_mcbond_it 0.585 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.759 r_dihedral_angle_4_deg 14.785 r_dihedral_angle_3_deg 12.833 r_dihedral_angle_1_deg 5.574 r_scangle_it 1.896 r_scbond_it 1.394 r_angle_refined_deg 1.218 r_mcangle_it 0.866 r_mcbond_it 0.585 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.206 r_nbd_refined 0.198 r_symmetry_hbond_refined 0.158 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.08 r_bond_refined_d 0.01 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_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 4528 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing