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Crystal structure of putative amidohydrolase-2 (EFI-target 500288)from Polaromonas sp. JS666
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DVT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.1M Tris hydrochloride, 2M Ammonium Sulfate, pH 8.5, Vapor diffusion, Sitting drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.7 54.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.024 α = 90 b = 151.241 β = 91.96 c = 143.41 γ = 90
Symmetry Space Group P 1 21 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 QUANTUM 315 2010-11-19 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9793 NSLS X29A
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 1.9 40 99.1 0.093 7.3 7.1 268076 268076
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 1.9 1.93 97.1 0.59 6.8 13135
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 2DVT 1.9 40 252922 12743 93.13 0.1766 0.1749 0.1897 0.2072 0.2202 RANDOM 24.684
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] -0.12 0.05 -0.57 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.293 r_dihedral_angle_4_deg 19.136 r_dihedral_angle_3_deg 13.457 r_dihedral_angle_1_deg 6.57 r_scangle_it 3.601 r_scbond_it 2.268 r_angle_refined_deg 1.38 r_mcangle_it 1.239 r_mcbond_it 0.7 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.293 r_dihedral_angle_4_deg 19.136 r_dihedral_angle_3_deg 13.457 r_dihedral_angle_1_deg 6.57 r_scangle_it 3.601 r_scbond_it 2.268 r_angle_refined_deg 1.38 r_mcangle_it 1.239 r_mcbond_it 0.7 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21079 Nucleic Acid Atoms Solvent Atoms 1513 Heterogen Atoms 338
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction MOLREP phasing