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Structure and a Proposed Mechanism for Ornithine Cyclodeaminase from Pseudomonas putida
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other EXPERIMENTAL PHASES
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.25 293 0.1M Na-MES and 40% MPD, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.1 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.9 α = 90 b = 78.6 β = 90 c = 119.9 γ = 90
Symmetry Space Group P 21 21 21
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 BRANDEIS - B4 DOUBLE-CRYSTAL MONOCHROMATOR SI(111), BEAM FOCUSED BY A TOROIDAL MIRROR. 2004-06-07 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 0.97946, 0.97888, 0.96114 NSLS X12C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.8 30 100 0.08 39.4 12.6 62180 -3 10.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.86 100 0.375 7.8 12
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 MAD THROUGHOUT EXPERIMENTAL PHASES 1.8 24.95 62014 61208 3102 98.7 0.158 0.159 0.181 0.1816 RANDOM 15.1
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] 0.65 -0.65
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.6 c_scangle_it 2.811 c_mcangle_it 1.996 c_scbond_it 1.54 c_angle_deg 1.4 c_mcbond_it 1.064 c_improper_angle_d 0.83 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.6 c_scangle_it 2.811 c_mcangle_it 1.996 c_scbond_it 1.54 c_angle_deg 1.4 c_mcbond_it 1.064 c_improper_angle_d 0.83 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5247 Nucleic Acid Atoms Solvent Atoms 789 Heterogen Atoms 90
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing ARP/wARP model building