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1-pyrroline-5-carboxylate dehydrogenase from Thermus thermophilus with bound inhibitor L-proline and NAD.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BJK PDB ENTRY 2BJK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.2 PROTEIN WAS CRYSTALLIZED FROM 37.5% MRD, 50 MM SODIUM CITRATE, PH 5.2; THEN SOAKED IN 2MM NAD, 100MM L-PROLINE, 50 MM SODIUM ACETATE PH5.2.
Crystal Properties Matthews coefficient Solvent content 2.4 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.043 α = 90 b = 102.043 β = 90 c = 278.6 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 RIGAKU CCD MIRRORS 2006-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 SPring-8 BL26B1
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 2.1 30 99.7 0.1 11.1 3.2 62989 -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 2.1 2.18 98.9 0.32 2 2.7
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BJK 2.1 30 59782 3193 99.7 0.142 0.14 0.1435 0.189 RANDOM 19.21
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] 1.32 0.66 1.32 -1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.976 r_dihedral_angle_4_deg 18.366 r_dihedral_angle_3_deg 13.903 r_dihedral_angle_1_deg 9.954 r_scangle_it 3.939 r_scbond_it 2.455 r_angle_refined_deg 1.536 r_mcangle_it 1.275 r_mcbond_it 0.707 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.976 r_dihedral_angle_4_deg 18.366 r_dihedral_angle_3_deg 13.903 r_dihedral_angle_1_deg 9.954 r_scangle_it 3.939 r_scbond_it 2.455 r_angle_refined_deg 1.536 r_mcangle_it 1.275 r_mcbond_it 0.707 r_nbtor_refined 0.308 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.189 r_xyhbond_nbd_refined 0.137 r_symmetry_hbond_refined 0.128 r_chiral_restr 0.103 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 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 8078 Nucleic Acid Atoms Solvent Atoms 788 Heterogen Atoms 170
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling REFMAC phasing