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Crystal structure of the r139n mutant of a bifunctional enzyme pria
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VEP PDB ENTRY 2VEP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.8 1.50 M AMMONIUM SULFATE AND 100 MM SODIUM CITRATE PH 4.8
Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.6 α = 90 b = 63.6 β = 90 c = 102.9 γ = 120
Symmetry Space Group P 31 2 1
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 CCD MIRRORS 2007-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 ESRF BM16
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 28 99.8 0.09 23 10.1 18061 -3 27.3
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 2.02 100 0.65 2.4 9.8
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2VEP 1.95 27.52 17365 696 99.62 0.21816 0.216 0.2155 0.2727 0.2693 RANDOM 39.217
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] 3.1 1.55 3.1 -4.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.29 r_dihedral_angle_4_deg 23.083 r_dihedral_angle_3_deg 16.552 r_dihedral_angle_1_deg 6.456 r_scangle_it 2.242 r_scbond_it 1.55 r_angle_refined_deg 1.389 r_mcangle_it 1.134 r_mcbond_it 0.69 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.29 r_dihedral_angle_4_deg 23.083 r_dihedral_angle_3_deg 16.552 r_dihedral_angle_1_deg 6.456 r_scangle_it 2.242 r_scbond_it 1.55 r_angle_refined_deg 1.389 r_mcangle_it 1.134 r_mcbond_it 0.69 r_nbtor_refined 0.298 r_symmetry_hbond_refined 0.216 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.195 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.09 r_bond_refined_d 0.016 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1709 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling