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Crystal analysis of delta1-pyrroline-5-carboxylate dehydrogenase from Thermus thermophilus with bound D-proline
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 VAPOR DIFFUSION, SITTING DROP 5.2 293 30% MPD, 50MM SODIUM CITRATE/HCL, PH5.2; THEN SOAKED IN 30% MPD,50mM D-proline, 50MM SODIUM Acetate, PH5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.39 48.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.761 α = 90 b = 100.761 β = 90 c = 279.93 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 ADSC QUANTUM 210 mirrors 2006-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 1.0 SPring-8 BL44B2
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 2.05 25 100 0.098 0.091 19 5.5 65727 65727 -3 17.1
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 2.05 2.12 100 0.446 0.414 4 5.1 6575
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 (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 PDB ENTRY 2bhp 2.06 24.68 60007 60007 3196 95.85 0.17312 0.16996 0.1685 0.23106 0.2253 RANDOM 23.327
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] 0.14 0.07 0.14 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.383 r_dihedral_angle_4_deg 17.781 r_dihedral_angle_3_deg 15.832 r_dihedral_angle_1_deg 7.063 r_scangle_it 4.645 r_scbond_it 2.93 r_angle_refined_deg 1.863 r_mcangle_it 1.576 r_mcbond_it 0.916 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.383 r_dihedral_angle_4_deg 17.781 r_dihedral_angle_3_deg 15.832 r_dihedral_angle_1_deg 7.063 r_scangle_it 4.645 r_scbond_it 2.93 r_angle_refined_deg 1.863 r_mcangle_it 1.576 r_mcbond_it 0.916 r_nbtor_refined 0.312 r_metal_ion_refined 0.231 r_symmetry_hbond_refined 0.211 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.194 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.121 r_bond_refined_d 0.021 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8076 Nucleic Acid Atoms Solvent Atoms 546 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement BSS data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing