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Resting Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 6.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3T63
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 1.2 M Ammonium Sulfate, 2.5 mM 2-mercaptoethanol, 100 mM MES pH 6.5; 2:1 ratio of well sol. to 40 mg/ml protein solution in drop
Crystal Properties Matthews coefficient Solvent content 2.58 52.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.919 α = 90 b = 140.767 β = 90 c = 168.191 γ = 90
Symmetry Space Group I 2 2 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 ADSC QUANTUM 315r 2014-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.54 50 93.4 0.124 0.139 0.061 12.1 5 206314
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.54 1.57 100 0.475 0.552 0.277 0.832 3.7 10956
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 3T63 1.541 39.02 195983 10324 92.96 0.1416 0.14 0.1395 0.1719 0.1718 RANDOM 21.072
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] -0.05 -0.17 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.034 r_sphericity_free 19.198 r_dihedral_angle_4_deg 15.687 r_dihedral_angle_3_deg 12.816 r_dihedral_angle_1_deg 6.541 r_sphericity_bonded 5.91 r_rigid_bond_restr 3.503 r_angle_refined_deg 1.332 r_angle_other_deg 0.812 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.034 r_sphericity_free 19.198 r_dihedral_angle_4_deg 15.687 r_dihedral_angle_3_deg 12.816 r_dihedral_angle_1_deg 6.541 r_sphericity_bonded 5.91 r_rigid_bond_restr 3.503 r_angle_refined_deg 1.332 r_angle_other_deg 0.812 r_chiral_restr 0.084 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10366 Nucleic Acid Atoms Solvent Atoms 1117 Heterogen Atoms 26
Software Software Software Name Purpose HKL-3000 data reduction REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data scaling DENZO data reduction SCALEPACK data scaling