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Refinement of Haemophilus influenzae Diaminopimelate epimerase at 1.7A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BWZ PDB ENTRY 1BWZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.1M IMIDIZOLE PH 6.5,
Crystal Properties Matthews coefficient Solvent content 2.64 53.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.637 α = 90 b = 113.87 β = 90 c = 64.481 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 290 1999-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 SRS PX9.6
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 1.75 56 99.2 0.039 29.98 2.4 37280 2
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 1.75 2 99.9 0.212 7.41 2
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 1BWZ 1.75 50 35201 1850 99.2 0.167 0.165 0.1757 0.196 0.2096 RANDOM 24.91
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 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.509 r_dihedral_angle_1_deg 5.394 r_scangle_it 5.201 r_scbond_it 3.284 r_mcangle_it 2.186 r_angle_refined_deg 1.707 r_mcbond_it 1.309 r_angle_other_deg 0.837 r_nbd_refined 0.23 r_symmetry_vdw_other 0.219
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.509 r_dihedral_angle_1_deg 5.394 r_scangle_it 5.201 r_scbond_it 3.284 r_mcangle_it 2.186 r_angle_refined_deg 1.707 r_mcbond_it 1.309 r_angle_other_deg 0.837 r_nbd_refined 0.23 r_symmetry_vdw_other 0.219 r_nbd_other 0.206 r_xyhbond_nbd_refined 0.188 r_symmetry_hbond_refined 0.129 r_chiral_restr 0.107 r_symmetry_vdw_refined 0.04 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_bond_refined_d r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 2083 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling