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Prolidase from Pyrococcus furiosus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 PEG 8000, magnesium acetate, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.41 49.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.476 α = 90 b = 97.227 β = 97.09 c = 69.882 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 4 2000-03-23 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 1.282, 1.283, 1.240, 1.333 SSRL BL9-2
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 1.95 50 94.9 0.035 26.8 3.8 54629 51843
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 1.95 2.02 94.1 0.334 2.98 3.4 5106
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2 20 45667 45667 2432 96.82 0.24637 0.24637 0.24473 0.3127 0.27727 RANDOM 21.52
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] 2.26 2.01 -2.8 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.501 r_scangle_it 1.92 r_scbond_it 1.25 r_mcangle_it 0.886 r_angle_refined_deg 0.848 r_mcbond_it 0.469 r_nbd_refined 0.161 r_symmetry_vdw_refined 0.136 r_xyhbond_nbd_refined 0.094 r_chiral_restr 0.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.501 r_scangle_it 1.92 r_scbond_it 1.25 r_mcangle_it 0.886 r_angle_refined_deg 0.848 r_mcbond_it 0.469 r_nbd_refined 0.161 r_symmetry_vdw_refined 0.136 r_xyhbond_nbd_refined 0.094 r_chiral_restr 0.056 r_symmetry_hbond_refined 0.036 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5196 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MLPHARE phasing