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Crystal structure of the bifunctional protein Pria
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H5Y PDB ENTRY 1H5Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 1.6 M NH4SO4 PH 5.5
Crystal Properties Matthews coefficient Solvent content 2.5 49.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.473 α = 90 b = 64.473 β = 90 c = 102.869 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 MARRESEARCH 2004-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 1.7 34.3 99.7 0.083 7.4463 3.93 27751
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 1.7 1.79 100 0.51 1.41 2.98
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-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 1H5Y 1.8 25 22242 1167 99.4 0.164 0.1779 0.205 0.2116 RANDOM 13.75
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] 0.86 0.43 0.86 -1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.051 r_scangle_it 5.003 r_scbond_it 3.261 r_mcangle_it 3.176 r_mcbond_it 2.134 r_angle_refined_deg 1.246 r_angle_other_deg 0.798 r_symmetry_vdw_other 0.264 r_nbd_other 0.24 r_nbd_refined 0.201
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.051 r_scangle_it 5.003 r_scbond_it 3.261 r_mcangle_it 3.176 r_mcbond_it 2.134 r_angle_refined_deg 1.246 r_angle_other_deg 0.798 r_symmetry_vdw_other 0.264 r_nbd_other 0.24 r_nbd_refined 0.201 r_symmetry_hbond_refined 0.162 r_xyhbond_nbd_refined 0.154 r_symmetry_vdw_refined 0.124 r_nbtor_other 0.081 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 1633 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing