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1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE FROM THERMUS THERMOPHIRUS WITH BOUND INHIBITOR GLYCINE AND NAD.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BHP PDB ENTRY 2BHP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.2 PROTEIN WAS CRYSTALLIZED FROM 37.5% MPD, 50 MM SODIUM CITRATE, PH 5.2; THEN SOAKED IN 5MM NAD, 50MM GLYCINE, 50 MM SODIUM ACETATE PH5.2.
Crystal Properties Matthews coefficient Solvent content 2.4 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.589 α = 90 b = 102.589 β = 90 c = 278.637 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-MSC MIRRORS 2006-06-03 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 1.63 30 99.7 0.07 23.2 4.4 135842 -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 1.63 1.67 95.9 0.38 2.3 3.7
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 2BHP 1.63 92.85 129001 6829 99.9 0.147 0.146 0.1443 0.174 RANDOM 13.48
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] 0.46 0.23 0.46 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.764 r_dihedral_angle_4_deg 15.44 r_dihedral_angle_3_deg 11.888 r_dihedral_angle_1_deg 6.076 r_scangle_it 3.067 r_scbond_it 1.783 r_angle_refined_deg 1.224 r_mcangle_it 0.941 r_mcbond_it 0.487 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.764 r_dihedral_angle_4_deg 15.44 r_dihedral_angle_3_deg 11.888 r_dihedral_angle_1_deg 6.076 r_scangle_it 3.067 r_scbond_it 1.783 r_angle_refined_deg 1.224 r_mcangle_it 0.941 r_mcbond_it 0.487 r_nbtor_refined 0.311 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.157 r_symmetry_hbond_refined 0.128 r_xyhbond_nbd_refined 0.107 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 8076 Nucleic Acid Atoms Solvent Atoms 1163 Heterogen Atoms 188
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling REFMAC phasing