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Dehalogenase DPpA from Plesiocystis pacifica SIR-I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EDB PDB ENTRY 1EDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.1 M MES PH 6.5, 1.8M (NH4)2SO4, 5% PEG400
Crystal Properties Matthews coefficient Solvent content 2.6 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.262 α = 90 b = 108.501 β = 90 c = 67.312 γ = 90
Symmetry Space Group P 21 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 RIGAKU SATURN 92 OSMIC MULTILAYER OPTIC 2009-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 38.68 98.5 0.12 7 5.5 25613 26
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 97.4 0.44 2.3 4.1
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 1EDB 1.9 67.31 25826 1375 97.04 0.22081 0.21931 0.2189 0.24801 0.2487 RANDOM 20.519
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] 0.14 -0.21 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.324 r_dihedral_angle_4_deg 15.6 r_dihedral_angle_3_deg 13.979 r_dihedral_angle_1_deg 6.827 r_scangle_it 4.039 r_scbond_it 2.729 r_angle_refined_deg 1.854 r_mcangle_it 1.638 r_angle_other_deg 1.085 r_mcbond_it 1.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.324 r_dihedral_angle_4_deg 15.6 r_dihedral_angle_3_deg 13.979 r_dihedral_angle_1_deg 6.827 r_scangle_it 4.039 r_scbond_it 2.729 r_angle_refined_deg 1.854 r_mcangle_it 1.638 r_angle_other_deg 1.085 r_mcbond_it 1.072 r_mcbond_other 0.362 r_chiral_restr 0.118 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_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 2299 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction CrystalClear data scaling PHASER phasing