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Crystal structure of prolidase eah89906 complexed with n-methylphosphonate-l-proline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FEQ PDB ENTRY 3FEQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 8% PEG8000, MES, PH 6.0, 200MM SODIUM ACETATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 280K
Crystal Properties Matthews coefficient Solvent content 2.74 55.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.186 α = 81.32 b = 108.035 β = 80.47 c = 170.772 γ = 73.76
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 315 MIRRORS 2009-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
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 2.8 50 98.3 0.18 3.5 1.9 186340 -5 76.32
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 97 0.5 1.9
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MR THROUGHOUT PDB ENTRY 3FEQ 2.81 40 162394 5054 89.92 0.22182 0.22023 0.2293 0.27297 0.2762 RANDOM 85.979
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] 0.38 -1.23 2.2 0.38 -0.01 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.299 r_dihedral_angle_3_deg 18.639 r_dihedral_angle_4_deg 15.008 r_scangle_it 12.096 r_scbond_it 7.757 r_dihedral_angle_1_deg 5.551 r_mcangle_it 5.326 r_mcbond_it 3.008 r_angle_refined_deg 1.142 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.299 r_dihedral_angle_3_deg 18.639 r_dihedral_angle_4_deg 15.008 r_scangle_it 12.096 r_scbond_it 7.757 r_dihedral_angle_1_deg 5.551 r_mcangle_it 5.326 r_mcbond_it 3.008 r_angle_refined_deg 1.142 r_chiral_restr 0.077 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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 48528 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 224
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling