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Histidinol-phosphate aminotransferase from Corynebacterium glutamicum holo-form (PLP covalently bound )
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CQ5 PDB ENTRY 3CQ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.4M NaH2PO4, 1.6M K2HPO4, 0.2M NaCl, 0.1M imidazole, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.79 55.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 191.798 α = 90 b = 80.017 β = 94.79 c = 88.484 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 ADSC QUANTUM 315r 2006-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.939 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.1 88 96.9 0.09 0.09 10.4 2.6 75438 75438 28.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.21 96.8 0.45 0.45 1.8 2.6 10992
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 3CQ5 2.1 30.79 71661 71661 3751 96.68 0.19962 0.19962 0.19767 0.2063 0.23837 0.2443 RANDOM 24.872
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] 1.47 -0.49 1.55 -3.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.816 r_dihedral_angle_4_deg 22.122 r_dihedral_angle_3_deg 14.525 r_dihedral_angle_1_deg 5.632 r_scangle_it 2.302 r_scbond_it 1.536 r_angle_refined_deg 1.228 r_angle_other_deg 0.903 r_mcangle_it 0.854 r_mcbond_it 0.738
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.816 r_dihedral_angle_4_deg 22.122 r_dihedral_angle_3_deg 14.525 r_dihedral_angle_1_deg 5.632 r_scangle_it 2.302 r_scbond_it 1.536 r_angle_refined_deg 1.228 r_angle_other_deg 0.903 r_mcangle_it 0.854 r_mcbond_it 0.738 r_symmetry_vdw_other 0.287 r_nbd_refined 0.21 r_nbd_other 0.196 r_nbtor_refined 0.175 r_symmetry_hbond_refined 0.157 r_mcbond_other 0.146 r_xyhbond_nbd_refined 0.145 r_symmetry_vdw_refined 0.109 r_nbtor_other 0.086 r_chiral_restr 0.067 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8442 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement DNA data collection MOSFLM data reduction SCALA data scaling MOLREP phasing