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Crystal analysis of 1-pyrroline-5-carboxylate dehydrogenase from thermus with bound NAD and Inhibitor L-serine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.2 30% MPD, 50MM SODIUM CITRATE/HCL, 30% MPD, 5mM NAD+, 50mM L-serine, 50MM SODIUM Acetate, pH 5.2, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.47 50.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.556 α = 90 b = 102.556 β = 90 c = 278.585 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 JUPITER 210 mirrors 2006-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0 SPring-8 BL26B1
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 1.8 92.85 99.9 0.065 0.059 33.3 5.9 100690 100690 -3 14.5
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) 1 1.8 1.86 99.8 0.274 0.247 5.7 5.9 10046
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FOURIER SYNTHESIS THROUGHOUT 1.8 30 95665 95665 5024 99.81 0.14006 0.14006 0.13863 0.1376 0.16725 0.1655 RANDOM 13.871
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] 0.56 0.28 0.56 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.647 r_dihedral_angle_4_deg 17.053 r_dihedral_angle_3_deg 12.436 r_dihedral_angle_1_deg 6.071 r_scangle_it 3.397 r_scbond_it 2.003 r_angle_refined_deg 1.277 r_mcangle_it 1.05 r_mcbond_it 0.546 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.647 r_dihedral_angle_4_deg 17.053 r_dihedral_angle_3_deg 12.436 r_dihedral_angle_1_deg 6.071 r_scangle_it 3.397 r_scbond_it 2.003 r_angle_refined_deg 1.277 r_mcangle_it 1.05 r_mcbond_it 0.546 r_nbtor_refined 0.31 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.172 r_symmetry_hbond_refined 0.138 r_xyhbond_nbd_refined 0.118 r_metal_ion_refined 0.092 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8076 Nucleic Acid Atoms Solvent Atoms 988 Heterogen Atoms 224
Software Software Software Name Purpose REFMAC refinement BSS data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing