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Crystal structure of diaminopelargonic acid aminotransferase from Psychrobacter cryohalolentis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 6.1 293 Sodium Citrate 0.1M pH 6.1;
Potassium Sodium Tartrate 0.2M;
Ammonium sulfate 1.6M
Crystal Properties Matthews coefficient Solvent content 2.99 58.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.069 α = 90 b = 67.91 β = 128.81 c = 118.07 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 PIXEL DECTRIS PILATUS 6M-F 2016-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 70.94 97 0.106 0.115 0.045 0.997 10.6 6.4 143372
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 98.6 0.836 0.908 0.35 0.752 6.5
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 1QJ5 1.6 70.94 136275 7082 96.84 0.1489 0.1469 0.152 0.1883 0.1864 RANDOM 17.872
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] 4.72 5.28 -4.94 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.664 r_sphericity_free 34.911 r_dihedral_angle_4_deg 14.132 r_dihedral_angle_3_deg 13.123 r_sphericity_bonded 12.95 r_dihedral_angle_1_deg 6.418 r_rigid_bond_restr 3.449 r_angle_other_deg 2.131 r_angle_refined_deg 1.974 r_chiral_restr 0.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.664 r_sphericity_free 34.911 r_dihedral_angle_4_deg 14.132 r_dihedral_angle_3_deg 13.123 r_sphericity_bonded 12.95 r_dihedral_angle_1_deg 6.418 r_rigid_bond_restr 3.449 r_angle_other_deg 2.131 r_angle_refined_deg 1.974 r_chiral_restr 0.124 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6402 Nucleic Acid Atoms Solvent Atoms 742 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection BALBES phasing PDB_EXTRACT data extraction iMOSFLM data reduction Aimless data scaling