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Recombinant prolidase from Thermococcus sibiricus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HOW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 277 Protein solution (2mcl): 10.8 mg/mL Tsprol and 150 mM NaCl in 50 mM Tris buffer (pH 7.6). Reservoir solution (2mcl): 100 mM CdCl2 and 30 % v/v PEG400 in 100 mM sodium acetate buffer (pH 4.6), VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.9 68.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.7 α = 90 b = 89.7 β = 90 c = 165.22 γ = 90
Symmetry Space Group P 41 21 2
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 MAR CCD 165 mm 2010-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON KURCHATOV SNC BEAMLINE K4.4 0.9887 KURCHATOV SNC K4.4
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 2.6 78.83 99.2 0.089 24.5 21480 21360
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 2.6 2.8 99.8 0.728 4.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2HOW 2.6 78.83 20268 1092 99.44 0.23293 0.231 0.26859 0.222 RANDOM 49.071
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] 0.57 0.57 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.07 r_dihedral_angle_3_deg 19.525 r_dihedral_angle_4_deg 19.166 r_dihedral_angle_1_deg 6.142 r_scangle_it 2.91 r_scbond_it 1.799 r_angle_refined_deg 1.384 r_mcangle_it 1.276 r_mcbond_it 0.683 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.07 r_dihedral_angle_3_deg 19.525 r_dihedral_angle_4_deg 19.166 r_dihedral_angle_1_deg 6.142 r_scangle_it 2.91 r_scbond_it 1.799 r_angle_refined_deg 1.384 r_mcangle_it 1.276 r_mcbond_it 0.683 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2851 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 12
Software Software Software Name Purpose AUTOMAR data collection BALBES phasing REFMAC refinement XDS data reduction XSCALE data scaling